diff --git a/package.json b/package.json index 918cbcb..4e6e528 100644 --- a/package.json +++ b/package.json @@ -732,6 +732,7 @@ "test:perf": "mocha --require ts-node/register 'test/perf/**/*.test.ts' --timeout 60000", "test:webview": "cd webview && npm test", "coverage": "c8 npm run test:unit", + "fetch:fixtures": "ts-node scripts/fetch-real-fixtures.ts", "package": "vsce package" }, "devDependencies": { diff --git a/scripts/fetch-real-fixtures.ts b/scripts/fetch-real-fixtures.ts new file mode 100644 index 0000000..156c7a7 --- /dev/null +++ b/scripts/fetch-real-fixtures.ts @@ -0,0 +1,209 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// +// DEV-ONLY. Downloads and slices real-world fixtures declared in +// test/fixtures/real/sources.json, writes provenance, and pins sha256 back into +// the manifest. Requires network and (for indexed entries) `tabix`/`bgzip`. +// +// This script is NEVER run by the test suite or CI — tests read only the +// committed artifacts. Run manually: +// +// npm run fetch:fixtures # all entries +// npm run fetch:fixtures -- --only giab_hg002_vcf kg_1000g_chr22_vcf +// +import * as fs from 'fs'; +import * as path from 'path'; +import * as crypto from 'crypto'; +import * as readline from 'readline'; +import { spawn, spawnSync } from 'child_process'; + +const REPO_ROOT = path.resolve(__dirname, '..'); +const MANIFEST_PATH = path.join(REPO_ROOT, 'test', 'fixtures', 'real', 'sources.json'); +const PROVENANCE_DIR = path.join(REPO_ROOT, 'test', 'fixtures', 'real', 'provenance'); + +interface Entry { + id: string; + languageId: string; + license: string; + attribution: string; + build: string; + obtain: 'direct' | 'head' | 'grep-slice' | 'gunzip-grep-slice' | 'tabix'; + source: string; + region?: string; + sliceChromPrefix?: string; + sliceRows?: number; + headDataRows?: number; + out: string; + sha256: string; + expect: Record; +} + +interface Manifest { + version: number; + root: string; + entries: Entry[]; +} + +function sha256(file: string): string { + return crypto.createHash('sha256').update(fs.readFileSync(file)).digest('hex'); +} + +function ensureDir(file: string): void { + fs.mkdirSync(path.dirname(file), { recursive: true }); +} + +function curlTo(url: string, dest: string): void { + ensureDir(dest); + const r = spawnSync('curl', ['-sSL', '--fail', '--max-time', '600', url, '-o', dest], { + stdio: ['ignore', 'inherit', 'inherit'], + }); + if (r.status !== 0) throw new Error(`curl failed (${r.status}) for ${url}`); +} + +/** Stream lines from a plain or gzipped file, keeping comments plus a bounded + * set of data lines, then stop early. Returns the number of data lines kept. */ +async function sliceLines( + srcFile: string, + outFile: string, + opts: { gzip: boolean; chromPrefix?: string; dataRows: number } +): Promise { + ensureDir(outFile); + const input = opts.gzip + ? spawn('gzip', ['-dc', srcFile]).stdout! + : fs.createReadStream(srcFile); + const out = fs.createWriteStream(outFile); + const rl = readline.createInterface({ input, crlfDelay: Infinity }); + + let kept = 0; + for await (const line of rl) { + if (line.startsWith('#')) { + out.write(line + '\n'); + continue; + } + if (opts.chromPrefix && !line.startsWith(opts.chromPrefix)) continue; + out.write(line + '\n'); + if (++kept >= opts.dataRows) break; + } + // Break-then-close avoids "readline was closed" from closing mid-iteration. + rl.close(); + (input as unknown as { destroy?: () => void }).destroy?.(); + await new Promise((res) => out.end(res)); + return kept; +} + +function tabixSlice(source: string, region: string, outGz: string): void { + ensureDir(outGz); + // `tabix -h ` fetches the remote .tbi and range-reads over HTTP. + const r = spawnSync('bash', ['-c', `tabix -h "${source}" "${region}" | bgzip -c > "${outGz}"`], { + stdio: ['ignore', 'inherit', 'inherit'], + }); + // Remote tabix caches the downloaded index as .tbi in the cwd; drop it. + const cachedIndex = path.join(process.cwd(), path.basename(source) + '.tbi'); + if (fs.existsSync(cachedIndex)) fs.rmSync(cachedIndex, { force: true }); + if (r.status !== 0) throw new Error(`tabix slice failed for ${source} ${region}`); + const idx = spawnSync('tabix', ['-f', '-p', 'vcf', outGz], { stdio: 'inherit' }); + if (idx.status !== 0) throw new Error(`tabix reindex failed for ${outGz}`); +} + +function nonCommentRows(file: string, gzip: boolean): number { + const data = gzip + ? spawnSync('gzip', ['-dc', file], { maxBuffer: 1 << 30 }).stdout.toString() + : fs.readFileSync(file, 'utf8'); + return data.split(/\r?\n/).filter((l) => l.length > 0 && !l.startsWith('#')).length; +} + +async function processEntry(entry: Entry, tmpDir: string): Promise { + const outAbs = path.join(REPO_ROOT, entry.out); + const tmp = path.join(tmpDir, entry.id); + let command = ''; + + if (entry.obtain === 'direct') { + curlTo(entry.source, outAbs); + command = `curl -sSL ${entry.source} -o ${entry.out}`; + } else if (entry.obtain === 'head') { + curlTo(entry.source, tmp); + const kept = await sliceLines(tmp, outAbs, { gzip: false, dataRows: entry.headDataRows ?? 50 }); + command = `curl ${entry.source} | head (kept ${kept} data rows)`; + } else if (entry.obtain === 'grep-slice') { + curlTo(entry.source, tmp); + const kept = await sliceLines(tmp, outAbs, { + gzip: false, + chromPrefix: entry.sliceChromPrefix, + dataRows: entry.sliceRows ?? 200, + }); + command = `curl ${entry.source} | grep "^${entry.sliceChromPrefix}" (kept ${kept})`; + } else if (entry.obtain === 'gunzip-grep-slice') { + curlTo(entry.source, tmp + '.gz'); + const kept = await sliceLines(tmp + '.gz', outAbs, { + gzip: true, + chromPrefix: entry.sliceChromPrefix, + dataRows: entry.sliceRows ?? 300, + }); + command = `curl ${entry.source} | gzip -dc | grep "^${entry.sliceChromPrefix}" (kept ${kept})`; + } else if (entry.obtain === 'tabix') { + tabixSlice(entry.source, entry.region!, outAbs); + command = `tabix -h ${entry.source} ${entry.region} | bgzip; tabix -p vcf`; + } else { + throw new Error(`Unknown obtain type: ${entry.obtain}`); + } + + const hash = sha256(outAbs); + entry.sha256 = hash; + + fs.mkdirSync(PROVENANCE_DIR, { recursive: true }); + fs.writeFileSync( + path.join(PROVENANCE_DIR, `${entry.id}.json`), + JSON.stringify( + { + id: entry.id, + source: entry.source, + obtain: entry.obtain, + command, + out: entry.out, + sha256: hash, + license: entry.license, + attribution: entry.attribution, + build: entry.build, + generated_at_utc: new Date().toISOString(), + }, + null, + 2 + ) + '\n' + ); + + const rows = nonCommentRows(outAbs, outAbs.endsWith('.gz')); + console.log(` ok ${entry.id}: ${rows} data rows, sha256=${hash.slice(0, 12)}…`); +} + +async function main(): Promise { + const args = process.argv.slice(2); + const onlyIdx = args.indexOf('--only'); + const only = onlyIdx >= 0 ? new Set(args.slice(onlyIdx + 1)) : null; + + const manifest: Manifest = JSON.parse(fs.readFileSync(MANIFEST_PATH, 'utf8')); + const tmpDir = fs.mkdtempSync(path.join(require('os').tmpdir(), 'biofmt-fixtures-')); + + let ok = 0; + let failed = 0; + for (const entry of manifest.entries) { + if (only && !only.has(entry.id)) continue; + console.log(`==> ${entry.id} (${entry.obtain})`); + try { + await processEntry(entry, tmpDir); + ok++; + } catch (err) { + failed++; + console.error(` FAILED ${entry.id}: ${(err as Error).message}`); + } + } + + // Pin checksums for whatever succeeded. + fs.writeFileSync(MANIFEST_PATH, JSON.stringify(manifest, null, 2) + '\n'); + fs.rmSync(tmpDir, { recursive: true, force: true }); + console.log(`\nDone: ${ok} ok, ${failed} failed. Checksums pinned in sources.json.`); + if (failed > 0) process.exitCode = 1; +} + +main().catch((e) => { + console.error(e); + process.exit(1); +}); diff --git a/test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz b/test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz new file mode 100644 index 0000000..476ac7f Binary files /dev/null and b/test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz differ diff --git a/test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz.tbi b/test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz.tbi new file mode 100644 index 0000000..43240e8 Binary files /dev/null and b/test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz.tbi differ diff --git a/test/fixtures/real/ATTRIBUTION.md b/test/fixtures/real/ATTRIBUTION.md new file mode 100644 index 0000000..b09b7d8 --- /dev/null +++ b/test/fixtures/real/ATTRIBUTION.md @@ -0,0 +1,26 @@ +# Real fixture attribution + +The files under `test/fixtures/real/` are small, sliced excerpts of publicly +redistributable genomics data, vendored so BioFmt is tested against real +caller/portal output. Each is a generated artifact — see `sources.json` for the +authoritative source URL and extraction command, and `provenance/.json` for +the pinned checksum. Regenerate with `npm run fetch:fixtures` (dev only; the test +suite never fetches). + +Only redistribution-safe sources are vendored. Sources requiring API resolution, +site-specific redistribution terms, or restrictive licenses (e.g. Manta's +Polyform Strict, 10x Genomics site terms, controlled-access TCGA) are +intentionally excluded. + +| Directory | Source | License / terms | +|-----------|--------|-----------------| +| `deepvariant/` | Google DeepVariant golden test outputs | BSD-3-Clause | +| `freebayes/` | freebayes regression baseline | MIT | +| `gridss/` | GRIDSS example SV VCF | GPL-3.0 | +| `giab/` | NIST Genome in a Bottle HG002 (NISTv4.2.1, GRCh38) | Public benchmark, consented for redistribution | +| `1000g/` | IGSR / 1000 Genomes Project phase 3 (20130502) | Open data | +| `gencode/` | GENCODE release 50 (basic annotation) | GENCODE / EMBL-EBI open | +| `ucsc/` | UCSC Genome Browser (chrom.sizes, bigPsl example) | UCSC open download | + +Each source retains its own upstream license; this directory does not relicense +the data. BioFmt itself is GPL-3.0. diff --git a/test/fixtures/real/deepvariant/golden.gvcf.g.vcf b/test/fixtures/real/deepvariant/golden.gvcf.g.vcf new file mode 100644 index 0000000..5076a67 --- /dev/null +++ b/test/fixtures/real/deepvariant/golden.gvcf.g.vcf @@ -0,0 +1,249 @@ +##fileformat=VCFv4.2 +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##DeepVariant_version=1.9.0 +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +chr20 10000000 . T <*> 0 . END=10000116 GT:GQ:MIN_DP:PL 0/0:50:45:0,135,1349 +chr20 10000117 . C T,<*> 37.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:55:25,30,0:0.545455,0:37,0,42,990,990,990 +chr20 10000118 . T <*> 0 . END=10000210 GT:GQ:MIN_DP:PL 0/0:50:50:0,171,1709 +chr20 10000211 . C T,<*> 37.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:38:59:30,29,0:0.491525,0:37,0,48,990,990,990 +chr20 10000212 . A <*> 0 . END=10000438 GT:GQ:MIN_DP:PL 0/0:50:50:0,174,1739 +chr20 10000439 . T G,<*> 45.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:43:72:0,72,0:1,0:45,46,0,990,990,990 +chr20 10000440 . T <*> 0 . END=10000597 GT:GQ:MIN_DP:PL 0/0:50:42:0,225,2249 +chr20 10000598 . T A,<*> 52.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:46:0,46,0:1,0:52,49,0,990,990,990 +chr20 10000599 . T <*> 0 . END=10000693 GT:GQ:MIN_DP:PL 0/0:50:44:0,135,1349 +chr20 10000694 . G A,<*> 7.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:7:48:26,22,0:0.458333,0:6,0,17,990,990,990 +chr20 10000695 . G <*> 0 . END=10000757 GT:GQ:MIN_DP:PL 0/0:50:46:0,147,1469 +chr20 10000758 . T A,<*> 42.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:56:0,56,0:1,0:42,32,0,990,990,990 +chr20 10000759 . A <*> 0 . END=10000999 GT:GQ:MIN_DP:PL 0/0:50:27:0,171,1709 +chr20 10001000 . G <*> 0 . END=10001018 GT:GQ:MIN_DP:PL 0/0:50:42:0,129,1289 +chr20 10001019 . T G,<*> 2.8 RefCall . GT:GQ:DP:AD:VAF:PL ./.:3:44:31,13,0:0.295455,0:0,0,19,990,990,990 +chr20 10001020 . C <*> 0 . END=10001080 GT:GQ:MIN_DP:PL 0/0:50:24:0,129,1289 +chr20 10001081 . T <*> 0 . END=10001081 GT:GQ:MIN_DP:PL 0/0:45:25:0,45,689 +chr20 10001082 . A <*> 0 . END=10001297 GT:GQ:MIN_DP:PL 0/0:50:25:0,81,809 +chr20 10001298 . T A,<*> 43.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:43:0,43,0:1,0:43,36,0,990,990,990 +chr20 10001299 . C <*> 0 . END=10001435 GT:GQ:MIN_DP:PL 0/0:50:29:0,138,1379 +chr20 10001436 . A AAGGCT,<*> 34.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:34:39:2,35,0:0.897436,0:34,39,0,990,990,990 +chr20 10001437 . A <*> 0 . END=10001473 GT:GQ:MIN_DP:PL 0/0:50:33:0,111,1109 +chr20 10001474 . C T,<*> 50.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:36:0,36,0:1,0:50,48,0,990,990,990 +chr20 10001475 . G <*> 0 . END=10001616 GT:GQ:MIN_DP:PL 0/0:50:37:0,111,1109 +chr20 10001617 . C A,<*> 33.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:34:43:23,20,0:0.465116,0:33,0,46,990,990,990 +chr20 10001618 . T <*> 0 . END=10001627 GT:GQ:MIN_DP:PL 0/0:50:40:0,123,1229 +chr20 10001628 . G A,<*> 54.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:44:0,44,0:1,0:54,56,0,990,990,990 +chr20 10001629 . G <*> 0 . END=10001660 GT:GQ:MIN_DP:PL 0/0:50:38:0,129,1289 +chr20 10001661 . T C,<*> 53.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:47:0,47,0:1,0:53,53,0,990,990,990 +chr20 10001662 . T <*> 0 . END=10001669 GT:GQ:MIN_DP:PL 0/0:50:47:0,147,1469 +chr20 10001670 . T G,<*> 48.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:46:0,46,0:1,0:48,49,0,990,990,990 +chr20 10001671 . G <*> 0 . END=10001999 GT:GQ:MIN_DP:PL 0/0:50:34:0,138,1379 +chr20 10002000 . T <*> 0 . END=10002057 GT:GQ:MIN_DP:PL 0/0:50:45:0,138,1379 +chr20 10002058 . T G,<*> 48.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:58:0,58,0:1,0:48,47,0,990,990,990 +chr20 10002059 . A <*> 0 . END=10002098 GT:GQ:MIN_DP:PL 0/0:50:58:0,177,1769 +chr20 10002099 . C T,<*> 10.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:11:57:27,30,0:0.526316,0:10,0,26,990,990,990 +chr20 10002100 . T <*> 0 . END=10002137 GT:GQ:MIN_DP:PL 0/0:50:45:0,174,1739 +chr20 10002138 . C G,<*> 51.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:47:0,47,0:1,0:51,50,0,990,990,990 +chr20 10002139 . A <*> 0 . END=10002141 GT:GQ:MIN_DP:PL 0/0:50:45:0,138,1379 +chr20 10002142 . G C,<*> 51.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:47:0,47,0:1,0:51,49,0,990,990,990 +chr20 10002143 . T <*> 0 . END=10002457 GT:GQ:MIN_DP:PL 0/0:50:36:0,144,1439 +chr20 10002458 . G GTT,GTTT,<*> 29.7 PASS . GT:GQ:DP:AD:VAF:PL 1/2:7:53:3,27,15,0:0.509434,0.283019,0:28,26,7,26,0,15,990,990,990,990 +chr20 10002459 . T <*> 0 . END=10002469 GT:GQ:MIN_DP:PL 0/0:50:46:0,150,1499 +chr20 10002470 . C T,<*> 39.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:42:0,42,0:1,0:39,38,0,990,990,990 +chr20 10002471 . T <*> 0 . END=10002481 GT:GQ:MIN_DP:PL 0/0:50:29:0,129,1289 +chr20 10002482 . G <*> 0 . END=10002482 GT:GQ:MIN_DP:PL 0/0:18:36:0,18,899 +chr20 10002483 . A <*> 0 . END=10002483 GT:GQ:MIN_DP:PL 0/0:27:29:0,27,749 +chr20 10002484 . T <*> 0 . END=10002492 GT:GQ:MIN_DP:PL 0/0:50:34:0,72,959 +chr20 10002493 . A C,<*> 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:42:37:32,5,0:0.135135,0:0,45,44,990,990,990 +chr20 10002494 . C <*> 0 . END=10002497 GT:GQ:MIN_DP:PL 0/0:48:36:0,48,959 +chr20 10002498 . G <*> 0 . END=10002498 GT:GQ:MIN_DP:PL 0/0:21:37:0,21,929 +chr20 10002499 . T <*> 0 . END=10002504 GT:GQ:MIN_DP:PL 0/0:50:42:0,150,1499 +chr20 10002505 . A <*> 0 . END=10002505 GT:GQ:MIN_DP:PL 0/0:39:43:0,39,1109 +chr20 10002506 . T <*> 0 . END=10002536 GT:GQ:MIN_DP:PL 0/0:50:39:0,129,1289 +chr20 10002537 . T <*> 0 . END=10002537 GT:GQ:MIN_DP:PL 0/0:36:52:0,36,1319 +chr20 10002538 . C <*> 0 . END=10002624 GT:GQ:MIN_DP:PL 0/0:50:44:0,171,1709 +chr20 10002625 . G T,<*> 47.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:55:0,55,0:1,0:47,47,0,990,990,990 +chr20 10002626 . G <*> 0 . END=10002999 GT:GQ:MIN_DP:PL 0/0:50:37:0,162,1619 +chr20 10003000 . A <*> 0 . END=10003020 GT:GQ:MIN_DP:PL 0/0:50:37:0,141,1409 +chr20 10003021 . C T,<*> 54.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:38:0,38,0:1,0:54,54,0,990,990,990 +chr20 10003022 . G <*> 0 . END=10003108 GT:GQ:MIN_DP:PL 0/0:50:27:0,114,1139 +chr20 10003109 . A C,<*> 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:46:32:28,4,0:0.125,0:0,48,49,990,990,990 +chr20 10003110 . C <*> 0 . END=10003357 GT:GQ:MIN_DP:PL 0/0:50:34:0,123,1229 +chr20 10003358 . A C,<*> 43.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:43:51:24,27,0:0.529412,0:43,0,53,990,990,990 +chr20 10003359 . C <*> 0 . END=10003650 GT:GQ:MIN_DP:PL 0/0:50:31:0,141,1409 +chr20 10003651 . T C,<*> 55.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:53:44:0,44,0:1,0:55,57,0,990,990,990 +chr20 10003652 . C <*> 0 . END=10003691 GT:GQ:MIN_DP:PL 0/0:50:42:0,132,1319 +chr20 10003692 . A G,<*> 58.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:53:44:0,44,0:1,0:58,54,0,990,990,990 +chr20 10003693 . T <*> 0 . END=10003831 GT:GQ:MIN_DP:PL 0/0:50:35:0,126,1259 +chr20 10003832 . G A,<*> 52.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:37:0,37,0:1,0:52,49,0,990,990,990 +chr20 10003833 . T <*> 0 . END=10003999 GT:GQ:MIN_DP:PL 0/0:50:38:0,117,1169 +chr20 10004000 . G <*> 0 . END=10004093 GT:GQ:MIN_DP:PL 0/0:50:35:0,141,1409 +chr20 10004094 . A C,<*> 51.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:35:0,35,0:1,0:51,52,0,990,990,990 +chr20 10004095 . C <*> 0 . END=10004146 GT:GQ:MIN_DP:PL 0/0:50:29:0,105,1049 +chr20 10004147 . A G,<*> 51.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:41:0,41,0:1,0:51,52,0,990,990,990 +chr20 10004148 . G <*> 0 . END=10004152 GT:GQ:MIN_DP:PL 0/0:50:41:0,129,1289 +chr20 10004153 . C <*> 0 . END=10004153 GT:GQ:MIN_DP:PL 0/0:33:41:0,33,1049 +chr20 10004154 . G <*> 0 . END=10004181 GT:GQ:MIN_DP:PL 0/0:50:36:0,141,1409 +chr20 10004182 . A <*> 0 . END=10004182 GT:GQ:MIN_DP:PL 0/0:33:41:0,33,1049 +chr20 10004183 . C <*> 0 . END=10004186 GT:GQ:MIN_DP:PL 0/0:50:38:0,126,1259 +chr20 10004187 . A <*> 0 . END=10004187 GT:GQ:MIN_DP:PL ./.:1:39:2,0,932 +chr20 10004188 . C <*> 0 . END=10004188 GT:GQ:MIN_DP:PL 0/0:50:44:0,132,1319 +chr20 10004189 . T <*> 0 . END=10004189 GT:GQ:MIN_DP:PL ./.:0:44:47,0,1007 +chr20 10004190 . C <*> 0 . END=10004192 GT:GQ:MIN_DP:PL 0/0:50:42:0,153,1529 +chr20 10004193 . G T,<*> 35 PASS . GT:GQ:DP:AD:VAF:PL 0/1:32:43:19,21,0:0.488372,0:35,0,36,990,990,990 +chr20 10004194 . C <*> 0 . END=10004207 GT:GQ:MIN_DP:PL 0/0:50:40:0,147,1469 +chr20 10004208 . T <*> 0 . END=10004208 GT:GQ:MIN_DP:PL 0/0:36:42:0,36,1079 +chr20 10004209 . G <*> 0 . END=10004214 GT:GQ:MIN_DP:PL 0/0:50:40:0,144,1439 +chr20 10004215 . C <*> 0 . END=10004215 GT:GQ:MIN_DP:PL 0/0:30:40:0,30,1019 +chr20 10004216 . T <*> 0 . END=10004216 GT:GQ:MIN_DP:PL 0/0:50:51:0,123,1469 +chr20 10004217 . G <*> 0 . END=10004217 GT:GQ:MIN_DP:PL 0/0:30:40:0,30,1019 +chr20 10004218 . T <*> 0 . END=10004221 GT:GQ:MIN_DP:PL 0/0:50:35:0,141,1409 +chr20 10004222 . C CA,<*> 18.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:18:51:19,28,0:0.54902,0:18,0,25,990,990,990 +chr20 10004223 . A AG,<*> 15.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:16:50:35,15,0:0.3,0:15,0,28,990,990,990 +chr20 10004224 . A <*> 0 . END=10004252 GT:GQ:MIN_DP:PL 0/0:50:42:0,138,1619 +chr20 10004253 . A T,<*> 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:44:55:48,7,0:0.127273,0:0,46,47,990,990,990 +chr20 10004254 . T <*> 0 . END=10004255 GT:GQ:MIN_DP:PL 0/0:50:66:0,198,1979 +chr20 10004256 . A <*> 0 . END=10004256 GT:GQ:MIN_DP:PL ./.:1:58:5,0,1385 +chr20 10004257 . T <*> 0 . END=10004350 GT:GQ:MIN_DP:PL 0/0:50:47:0,201,2009 +chr20 10004351 . C G,<*> 43.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:40:50:0,50,0:1,0:43,43,0,990,990,990 +chr20 10004352 . A <*> 0 . END=10004388 GT:GQ:MIN_DP:PL 0/0:50:39:0,147,1469 +chr20 10004389 . T G,<*> 48.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:41:0,41,0:1,0:48,47,0,990,990,990 +chr20 10004390 . G <*> 0 . END=10004609 GT:GQ:MIN_DP:PL 0/0:50:40:0,126,1259 +chr20 10004610 . A C,<*> 51.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:51:0,51,0:1,0:51,50,0,990,990,990 +chr20 10004611 . C <*> 0 . END=10004724 GT:GQ:MIN_DP:PL 0/0:50:44:0,156,1559 +chr20 10004725 . A G,<*> 29.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:16:51:27,24,0:0.470588,0:29,0,16,990,990,990 +chr20 10004726 . T <*> 0 . END=10004768 GT:GQ:MIN_DP:PL 0/0:50:49:0,150,1499 +chr20 10004769 . TAAAACTATGC T,<*> 43.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:41:53:14,39,0:0.735849,0:43,0,44,990,990,990 +chr20 10004780 . A <*> 0 . END=10004873 GT:GQ:MIN_DP:PL 0/0:50:53:0,162,1619 +chr20 10004874 . A C,<*> 47.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:43:58:0,58,0:1,0:47,45,0,990,990,990 +chr20 10004875 . T <*> 0 . END=10004886 GT:GQ:MIN_DP:PL 0/0:50:57:0,177,1769 +chr20 10004887 . A G,<*> 40.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:40:57:30,27,0:0.473684,0:40,0,51,990,990,990 +chr20 10004888 . A <*> 0 . END=10004999 GT:GQ:MIN_DP:PL 0/0:50:34:0,174,1739 +chr20 10005000 . G <*> 0 . END=10005009 GT:GQ:MIN_DP:PL 0/0:50:56:0,168,1679 +chr20 10005010 . C T,<*> 53.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:54:0,54,0:1,0:53,54,0,990,990,990 +chr20 10005011 . G <*> 0 . END=10005426 GT:GQ:MIN_DP:PL 0/0:50:43:0,168,1679 +chr20 10005427 . C T,<*> 52 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:44:0,44,0:1,0:51,47,0,990,990,990 +chr20 10005428 . A <*> 0 . END=10005498 GT:GQ:MIN_DP:PL 0/0:50:31:0,132,1319 +chr20 10005499 . A G,<*> 56.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:45:0,45,0:1,0:56,54,0,990,990,990 +chr20 10005500 . T <*> 0 . END=10005586 GT:GQ:MIN_DP:PL 0/0:50:45:0,141,1409 +chr20 10005587 . A G,<*> 44.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:43:61:31,30,0:0.491803,0:44,0,50,990,990,990 +chr20 10005588 . A <*> 0 . END=10005722 GT:GQ:MIN_DP:PL 0/0:50:48:0,180,1799 +chr20 10005723 . A G,<*> 52.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:53:0,53,0:1,0:52,53,0,990,990,990 +chr20 10005724 . A <*> 0 . END=10005999 GT:GQ:MIN_DP:PL 0/0:50:46:0,159,1589 +chr20 10006000 . G <*> 0 . END=10006290 GT:GQ:MIN_DP:PL 0/0:50:47:0,186,1859 +chr20 10006291 . G A,<*> 38.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:38:55:29,26,0:0.472727,0:38,0,49,990,990,990 +chr20 10006292 . A <*> 0 . END=10006403 GT:GQ:MIN_DP:PL 0/0:50:48:0,168,1679 +chr20 10006404 . A C,<*> 56.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:54:50:0,50,0:1,0:56,57,0,990,990,990 +chr20 10006405 . C <*> 0 . END=10006681 GT:GQ:MIN_DP:PL 0/0:50:42:0,150,1499 +chr20 10006682 . T A,<*> 51.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:47:0,47,0:1,0:51,50,0,990,990,990 +chr20 10006683 . A <*> 0 . END=10006818 GT:GQ:MIN_DP:PL 0/0:50:39:0,138,1379 +chr20 10006819 . AAAAC A,<*> 48.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:43:44:0,44,0:1,0:48,44,0,990,990,990 +chr20 10006824 . A <*> 0 . END=10006999 GT:GQ:MIN_DP:PL 0/0:50:35:0,135,1349 +chr20 10007000 . T <*> 0 . END=10007149 GT:GQ:MIN_DP:PL 0/0:50:43:0,165,1649 +chr20 10007150 . G C,<*> 31.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:32:46:29,17,0:0.369565,0:31,0,44,990,990,990 +chr20 10007151 . G <*> 0 . END=10007174 GT:GQ:MIN_DP:PL 0/0:50:43:0,144,1439 +chr20 10007175 . C T,<*> 46.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:46:45:22,23,0:0.511111,0:46,0,55,990,990,990 +chr20 10007176 . T <*> 0 . END=10007351 GT:GQ:MIN_DP:PL 0/0:50:38:0,135,1349 +chr20 10007352 . C T,<*> 57.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:54:45:0,45,0:1,0:57,57,0,990,990,990 +chr20 10007353 . A <*> 0 . END=10007530 GT:GQ:MIN_DP:PL 0/0:50:42:0,135,1349 +chr20 10007531 . A G,<*> 48.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:51:0,51,0:1,0:48,45,0,990,990,990 +chr20 10007532 . G <*> 0 . END=10007979 GT:GQ:MIN_DP:PL 0/0:50:30:0,147,1469 +chr20 10007980 . A C,<*> 53.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:61:0,61,0:1,0:53,57,0,990,990,990 +chr20 10007981 . A <*> 0 . END=10007999 GT:GQ:MIN_DP:PL 0/0:50:56:0,180,1799 +chr20 10008000 . G <*> 0 . END=10008028 GT:GQ:MIN_DP:PL 0/0:50:43:0,174,1739 +chr20 10008029 . T TA,<*> 51.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:43:0,43,0:1,0:51,46,0,990,990,990 +chr20 10008030 . A <*> 0 . END=10008145 GT:GQ:MIN_DP:PL 0/0:50:30:0,126,1259 +chr20 10008146 . TA T,<*> 53.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:46:0,46,0:1,0:53,55,0,990,990,990 +chr20 10008148 . A <*> 0 . END=10008220 GT:GQ:MIN_DP:PL 0/0:50:44:0,141,1409 +chr20 10008221 . T C,<*> 55.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:51:0,51,0:1,0:55,52,0,990,990,990 +chr20 10008222 . T <*> 0 . END=10008457 GT:GQ:MIN_DP:PL 0/0:50:33:0,156,1559 +chr20 10008458 . T G,<*> 53.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:36:0,36,0:1,0:53,53,0,990,990,990 +chr20 10008459 . A <*> 0 . END=10008675 GT:GQ:MIN_DP:PL 0/0:50:25:0,111,1109 +chr20 10008676 . A <*> 0 . END=10008676 GT:GQ:MIN_DP:PL 0/0:42:24:0,42,659 +chr20 10008677 . G <*> 0 . END=10008681 GT:GQ:MIN_DP:PL 0/0:50:22:0,75,749 +chr20 10008682 . A <*> 0 . END=10008682 GT:GQ:MIN_DP:PL 0/0:39:23:0,39,629 +chr20 10008683 . G <*> 0 . END=10008688 GT:GQ:MIN_DP:PL 0/0:50:20:0,63,629 +chr20 10008689 . T <*> 0 . END=10008689 GT:GQ:MIN_DP:PL 0/0:36:22:0,36,599 +chr20 10008690 . G <*> 0 . END=10008691 GT:GQ:MIN_DP:PL 0/0:50:24:0,78,779 +chr20 10008692 . A <*> 0 . END=10008692 GT:GQ:MIN_DP:PL 0/0:36:22:0,36,599 +chr20 10008693 . T <*> 0 . END=10008697 GT:GQ:MIN_DP:PL 0/0:50:20:0,60,599 +chr20 10008698 . A <*> 0 . END=10008698 GT:GQ:MIN_DP:PL 0/0:33:21:0,33,569 +chr20 10008699 . G <*> 0 . END=10008705 GT:GQ:MIN_DP:PL 0/0:50:19:0,75,749 +chr20 10008706 . A <*> 0 . END=10008706 GT:GQ:MIN_DP:PL 0/0:27:19:0,27,509 +chr20 10008707 . G <*> 0 . END=10008708 GT:GQ:MIN_DP:PL 0/0:50:19:0,57,569 +chr20 10008709 . T <*> 0 . END=10008709 GT:GQ:MIN_DP:PL 0/0:30:20:0,30,539 +chr20 10008710 . C <*> 0 . END=10008710 GT:GQ:MIN_DP:PL 0/0:50:22:0,66,659 +chr20 10008711 . G <*> 0 . END=10008711 GT:GQ:MIN_DP:PL 0/0:7:22:0,6,539 +chr20 10008712 . A <*> 0 . END=10008716 GT:GQ:MIN_DP:PL 0/0:50:23:0,78,779 +chr20 10008717 . AT A,<*> 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:39:25:23,2,0:0.08,0:0,40,46,990,990,990 +chr20 10008719 . C <*> 0 . END=10008723 GT:GQ:MIN_DP:PL 0/0:50:21:0,63,629 +chr20 10008724 . C <*> 0 . END=10008724 GT:GQ:MIN_DP:PL 0/0:18:26:0,18,659 +chr20 10008725 . T <*> 0 . END=10008729 GT:GQ:MIN_DP:PL 0/0:50:24:0,75,749 +chr20 10008730 . C <*> 0 . END=10008730 GT:GQ:MIN_DP:PL 0/0:45:25:0,45,689 +chr20 10008731 . A <*> 0 . END=10008732 GT:GQ:MIN_DP:PL 0/0:50:27:0,87,869 +chr20 10008733 . T <*> 0 . END=10008733 GT:GQ:MIN_DP:PL 0/0:9:23:0,9,569 +chr20 10008734 . G <*> 0 . END=10008734 GT:GQ:MIN_DP:PL 0/0:18:26:0,18,659 +chr20 10008735 . A <*> 0 . END=10008741 GT:GQ:MIN_DP:PL 0/0:50:26:0,93,929 +chr20 10008742 . G T,<*> 21.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:15:30:13,17,0:0.566667,0:21,0,15,990,990,990 +chr20 10008743 . T <*> 0 . END=10008744 GT:GQ:MIN_DP:PL 0/0:50:29:0,87,869 +chr20 10008745 . T <*> 0 . END=10008745 GT:GQ:MIN_DP:PL 0/0:45:25:0,45,689 +chr20 10008746 . C <*> 0 . END=10008749 GT:GQ:MIN_DP:PL 0/0:50:21:0,63,629 +chr20 10008750 . T TA,<*> 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:31:25:21,2,0:0.08,0:0,32,36,990,990,990 +chr20 10008751 . A <*> 0 . END=10008755 GT:GQ:MIN_DP:PL 0/0:50:30:0,102,1019 +chr20 10008756 . T <*> 0 . END=10008756 GT:GQ:MIN_DP:PL 0/0:3:20:0,0,479 +chr20 10008757 . A <*> 0 . END=10008757 GT:GQ:MIN_DP:PL 0/0:50:27:0,81,809 +chr20 10008758 . C CA,<*> 30.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:22:31:1,23,0:0.741935,0:30,22,0,990,990,990 +chr20 10008759 . A <*> 0 . END=10008878 GT:GQ:MIN_DP:PL 0/0:50:31:0,93,929 +chr20 10008879 . A <*> 0 . END=10008879 GT:GQ:MIN_DP:PL 0/0:4:31:0,3,749 +chr20 10008880 . C <*> 0 . END=10008913 GT:GQ:MIN_DP:PL 0/0:50:25:0,99,989 +chr20 10008914 . A <*> 0 . END=10008914 GT:GQ:MIN_DP:PL 0/0:15:25:0,15,629 +chr20 10008915 . C <*> 0 . END=10008920 GT:GQ:MIN_DP:PL 0/0:48:26:0,48,719 +chr20 10008921 . C CA,<*> 9.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:10:29:17,8,0:0.275862,0:9,0,33,990,990,990 +chr20 10008922 . A <*> 0 . END=10008947 GT:GQ:MIN_DP:PL 0/0:50:30:0,102,1019 +chr20 10008948 . TA T,<*> 34.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:40:0,40,0:1,0:34,30,0,990,990,990 +chr20 10008950 . A <*> 0 . END=10008951 GT:GQ:MIN_DP:PL 0/0:50:35:0,108,1079 +chr20 10008952 . CACACACACACA C,CCACACACACA,<*> 39.7 PASS . GT:GQ:DP:AD:VAF:PL 1/2:23:42:1,15,25,0:0.357143,0.595238,0:39,32,34,32,0,24,990,990,990,990 +chr20 10008964 . C <*> 0 . END=10008999 GT:GQ:MIN_DP:PL 0/0:50:23:0,69,689 +chr20 10009000 . T <*> 0 . END=10009226 GT:GQ:MIN_DP:PL 0/0:50:45:0,144,1439 +chr20 10009227 . A G,<*> 36.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:33:66:34,32,0:0.484848,0:36,0,35,990,990,990 +chr20 10009228 . G <*> 0 . END=10009245 GT:GQ:MIN_DP:PL 0/0:50:67:0,201,2009 +chr20 10009246 . A G,<*> 56.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:53:68:0,68,0:1,0:56,56,0,990,990,990 +chr20 10009247 . A <*> 0 . END=10009399 GT:GQ:MIN_DP:PL 0/0:50:58:0,201,2009 +chr20 10009400 . T A,<*> 43.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:70:0,70,0:1,0:43,45,0,990,990,990 +chr20 10009401 . A <*> 0 . END=10009511 GT:GQ:MIN_DP:PL 0/0:50:44:0,213,2129 +chr20 10009512 . C G,<*> 51.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:47:0,47,0:1,0:51,51,0,990,990,990 +chr20 10009513 . A <*> 0 . END=10009718 GT:GQ:MIN_DP:PL 0/0:50:33:0,144,1439 +chr20 10009719 . A G,<*> 52.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:33:0,33,0:1,0:52,49,0,990,990,990 +chr20 10009720 . T <*> 0 . END=10009794 GT:GQ:MIN_DP:PL 0/0:50:35:0,108,1079 +chr20 10009795 . A G,<*> 37.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:40:0,40,0:1,0:37,41,0,990,990,990 +chr20 10009796 . C <*> 0 . END=10009839 GT:GQ:MIN_DP:PL 0/0:50:38:0,120,1199 +chr20 10009840 . A <*> 0 . END=10009840 GT:GQ:MIN_DP:PL ./.:1:38:5,0,905 +chr20 10009841 . A <*> 0 . END=10009843 GT:GQ:MIN_DP:PL 0/0:50:38:0,117,1169 +chr20 10009844 . G A,<*> 12.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:4:41:10,31,0:0.756098,0:10,2,0,990,990,990 +chr20 10009845 . A <*> 0 . END=10009870 GT:GQ:MIN_DP:PL 0/0:50:41:0,126,1259 +chr20 10009871 . A G,<*> 18.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:15:47:9,38,0:0.808511,0:18,17,0,990,990,990 +chr20 10009872 . G <*> 0 . END=10009874 GT:GQ:MIN_DP:PL 0/0:50:39:0,150,1499 +chr20 10009875 . A G,<*> 21 PASS . GT:GQ:DP:AD:VAF:PL 1/1:17:52:7,44,0:0.846154,0:20,18,0,990,990,990 +chr20 10009876 . G <*> 0 . END=10009876 GT:GQ:MIN_DP:PL 0/0:50:51:0,153,1529 +chr20 10009877 . A G,<*> 0.2 RefCall . GT:GQ:DP:AD:VAF:PL ./.:14:38:33,5,0:0.131579,0:0,14,22,990,990,990 +chr20 10009878 . G <*> 0 . END=10009878 GT:GQ:MIN_DP:PL 0/0:50:50:0,150,1499 +chr20 10009879 . A G,<*> 31.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:28:48:0,47,0:0.979167,0:31,31,0,990,990,990 +chr20 10009880 . G <*> 0 . END=10009880 GT:GQ:MIN_DP:PL 0/0:50:51:0,153,1529 +chr20 10009881 . A <*> 0 . END=10009881 GT:GQ:MIN_DP:PL 0/0:27:39:0,27,989 +chr20 10009882 . G <*> 0 . END=10009882 GT:GQ:MIN_DP:PL 0/0:50:51:0,153,1529 +chr20 10009883 . A G,<*> 25.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:50:0,50,0:1,0:25,30,0,990,990,990 +chr20 10009884 . G <*> 0 . END=10009999 GT:GQ:MIN_DP:PL 0/0:50:34:0,87,1349 +chr20 10010000 . C <*> 0 . END=10010000 GT:GQ:MIN_DP:PL 0/0:50:61:0,183,1829 diff --git a/test/fixtures/real/deepvariant/golden.single_site.vcf b/test/fixtures/real/deepvariant/golden.single_site.vcf new file mode 100644 index 0000000..a426a5d --- /dev/null +++ b/test/fixtures/real/deepvariant/golden.single_site.vcf @@ -0,0 +1,99 @@ +##fileformat=VCFv4.2 +##FILTER= +##FILTER= +##FILTER= +##FILTER= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##DeepVariant_version=1.9.0 +##contig= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +chr20 10000117 . C T 37.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:55:25,30:0.545455:37,0,42 +chr20 10000211 . C T 37.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:38:59:30,29:0.491525:37,0,48 +chr20 10000439 . T G 45.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:43:72:0,72:1:45,46,0 +chr20 10000598 . T A 52.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:46:0,46:1:52,49,0 +chr20 10000694 . G A 7.4 PASS . GT:GQ:DP:AD:VAF:PL 0/1:7:48:26,22:0.458333:6,0,17 +chr20 10000758 . T A 42.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:32:56:0,56:1:42,32,0 +chr20 10001019 . T G 2.8 RefCall . GT:GQ:DP:AD:VAF:PL ./.:3:44:31,13:0.295455:0,0,19 +chr20 10001298 . T A 43.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:43:0,43:1:43,36,0 +chr20 10001436 . A AAGGCT 34.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:34:39:2,35:0.897436:34,39,0 +chr20 10001474 . C T 50.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:36:0,36:1:50,48,0 +chr20 10001617 . C A 33.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:34:43:23,20:0.465116:33,0,46 +chr20 10001628 . G A 54.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:44:0,44:1:54,56,0 +chr20 10001661 . T C 53.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:47:0,47:1:53,53,0 +chr20 10001670 . T G 48.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:46:0,46:1:48,49,0 +chr20 10002058 . T G 48.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:58:0,58:1:48,47,0 +chr20 10002099 . C T 10.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:11:57:27,30:0.526316:10,0,26 +chr20 10002138 . C G 51.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:47:0,47:1:51,50,0 +chr20 10002142 . G C 51.3 PASS . GT:GQ:DP:AD:VAF:PL 1/1:47:47:0,47:1:51,49,0 +chr20 10002458 . G GTT,GTTT 29.7 PASS . GT:GQ:DP:AD:VAF:PL 1/2:7:53:3,27,15:0.509434,0.283019:28,26,7,26,0,15 +chr20 10002470 . C T 39.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:42:0,42:1:39,38,0 +chr20 10002493 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:42:37:32,5:0.135135:0,45,44 +chr20 10002625 . G T 47.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:55:0,55:1:47,47,0 +chr20 10003021 . C T 54.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:38:0,38:1:54,54,0 +chr20 10003109 . A C 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:46:32:28,4:0.125:0,48,49 +chr20 10003358 . A C 43.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:43:51:24,27:0.529412:43,0,53 +chr20 10003651 . T C 55.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:53:44:0,44:1:55,57,0 +chr20 10003692 . A G 58.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:53:44:0,44:1:58,54,0 +chr20 10003832 . G A 52.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:37:0,37:1:52,49,0 +chr20 10004094 . A C 51.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:35:0,35:1:51,52,0 +chr20 10004147 . A G 51.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:49:41:0,41:1:51,52,0 +chr20 10004193 . G T 35 PASS . GT:GQ:DP:AD:VAF:PL 0/1:32:43:19,21:0.488372:35,0,36 +chr20 10004222 . C CA 18.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:18:51:19,28:0.54902:18,0,25 +chr20 10004223 . A AG 15.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:16:50:35,15:0.3:15,0,28 +chr20 10004253 . A T 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:44:55:48,7:0.127273:0,46,47 +chr20 10004351 . C G 43.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:40:50:0,50:1:43,43,0 +chr20 10004389 . T G 48.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:41:0,41:1:48,47,0 +chr20 10004610 . A C 51.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:51:0,51:1:51,50,0 +chr20 10004725 . A G 29.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:16:51:27,24:0.470588:29,0,16 +chr20 10004769 . TAAAACTATGC T 43.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:41:53:14,39:0.735849:43,0,44 +chr20 10004874 . A C 47.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:43:58:0,58:1:47,45,0 +chr20 10004887 . A G 40.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:40:57:30,27:0.473684:40,0,51 +chr20 10005010 . C T 53.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:54:0,54:1:53,54,0 +chr20 10005427 . C T 52 PASS . GT:GQ:DP:AD:VAF:PL 1/1:46:44:0,44:1:51,47,0 +chr20 10005499 . A G 56.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:45:0,45:1:56,54,0 +chr20 10005587 . A G 44.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:43:61:31,30:0.491803:44,0,50 +chr20 10005723 . A G 52.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:53:0,53:1:52,53,0 +chr20 10006291 . G A 38.3 PASS . GT:GQ:DP:AD:VAF:PL 0/1:38:55:29,26:0.472727:38,0,49 +chr20 10006404 . A C 56.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:54:50:0,50:1:56,57,0 +chr20 10006682 . T A 51.4 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:47:0,47:1:51,50,0 +chr20 10006819 . AAAAC A 48.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:43:44:0,44:1:48,44,0 +chr20 10007150 . G C 31.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:32:46:29,17:0.369565:31,0,44 +chr20 10007175 . C T 46.2 PASS . GT:GQ:DP:AD:VAF:PL 0/1:46:45:22,23:0.511111:46,0,55 +chr20 10007352 . C T 57.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:54:45:0,45:1:57,57,0 +chr20 10007531 . A G 48.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:44:51:0,51:1:48,45,0 +chr20 10007980 . A C 53.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:61:0,61:1:53,57,0 +chr20 10008029 . T TA 51.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:45:43:0,43:1:51,46,0 +chr20 10008146 . TA T 53.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:52:46:0,46:1:53,55,0 +chr20 10008221 . T C 55.8 PASS . GT:GQ:DP:AD:VAF:PL 1/1:51:51:0,51:1:55,52,0 +chr20 10008458 . T G 53.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:50:36:0,36:1:53,53,0 +chr20 10008717 . AT A 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:39:25:23,2:0.08:0,40,46 +chr20 10008742 . G T 21.5 PASS . GT:GQ:DP:AD:VAF:PL 0/1:15:30:13,17:0.566667:21,0,15 +chr20 10008750 . T TA 0 RefCall . GT:GQ:DP:AD:VAF:PL 0/0:31:25:21,2:0.08:0,32,36 +chr20 10008758 . C CA 30.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:22:31:1,23:0.741935:30,22,0 +chr20 10008921 . C CA 9.8 PASS . GT:GQ:DP:AD:VAF:PL 0/1:10:29:17,8:0.275862:9,0,33 +chr20 10008948 . TA T 34.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:29:40:0,40:1:34,30,0 +chr20 10008952 . CACACACACACA C,CCACACACACA 39.7 PASS . GT:GQ:DP:AD:VAF:PL 1/2:23:42:1,15,25:0.357143,0.595238:39,32,34,32,0,24 +chr20 10009227 . A G 36.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:33:66:34,32:0.484848:36,0,35 +chr20 10009246 . A G 56.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:53:68:0,68:1:56,56,0 +chr20 10009400 . T A 43.9 PASS . GT:GQ:DP:AD:VAF:PL 1/1:42:70:0,70:1:43,45,0 +chr20 10009512 . C G 51.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:47:0,47:1:51,51,0 +chr20 10009719 . A G 52.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:48:33:0,33:1:52,49,0 +chr20 10009795 . A G 37.5 PASS . GT:GQ:DP:AD:VAF:PL 1/1:36:40:0,40:1:37,41,0 +chr20 10009844 . G A 12.7 PASS . GT:GQ:DP:AD:VAF:PL 1/1:4:41:10,31:0.756098:10,2,0 +chr20 10009871 . A G 18.2 PASS . GT:GQ:DP:AD:VAF:PL 1/1:15:47:9,38:0.808511:18,17,0 +chr20 10009875 . A G 21 PASS . GT:GQ:DP:AD:VAF:PL 1/1:17:52:7,44:0.846154:20,18,0 +chr20 10009877 . A G 0.2 RefCall . GT:GQ:DP:AD:VAF:PL ./.:14:38:33,5:0.131579:0,14,22 +chr20 10009879 . A G 31.1 PASS . GT:GQ:DP:AD:VAF:PL 1/1:28:48:0,47:0.979167:31,31,0 +chr20 10009883 . A G 25.6 PASS . GT:GQ:DP:AD:VAF:PL 1/1:24:50:0,50:1:25,30,0 diff --git a/test/fixtures/real/freebayes/tiny_chr22.vcf b/test/fixtures/real/freebayes/tiny_chr22.vcf new file mode 100644 index 0000000..0a8da57 --- /dev/null +++ b/test/fixtures/real/freebayes/tiny_chr22.vcf @@ -0,0 +1,74 @@ +##fileformat=VCFv4.2 +##fileDate=20260308 +##source=freeBayes v1.3.10 +##reference=/home/hasitha/data/projects/freebayes/test/tiny/q.fa +##contig= +##phasing=none +##commandline="/home/hasitha/data/projects/freebayes/test/../build/freebayes -f /home/hasitha/data/projects/freebayes/test/tiny/q.fa -r q:1-1000 /home/hasitha/data/projects/freebayes/test/tiny/NA12878.chr22.tiny.bam" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1 +q 186 . T C 343.484 . AB=0.390244;ABP=7.30028;AC=1;AF=0.5;AN=2;AO=16;CIGAR=1X;DP=41;DPB=41;DPRA=0;EPP=3.55317;EPPR=7.26639;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=79.09;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=591;QR=953;RO=25;RPL=4;RPP=11.6962;RPPR=10.0459;RPR=12;RUN=1;SAF=11;SAP=7.89611;SAR=5;SRF=9;SRP=7.26639;SRR=16;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/1:41:25,16:25:953:16:591:-41.1681,0,-73.7281 +q 382 . C G 1.05177e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=35;DPB=35;DPRA=0;EPP=7.35324;EPPR=4.65535;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.5524;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=73;QR=1275;RO=33;RPL=1;RPP=3.0103;RPPR=4.65535;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=21;SRP=8.34028;SRR=12;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:35:33,2:33:1275:2:73:0,-3.60598,-108.099 +q 910 . A C 1.9784e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.73412;EPPR=4.65535;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=40.0086;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=45;QR=899;RO=33;RPL=2;RPP=3.73412;RPPR=17.8158;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=18;SRP=3.60252;SRR=15;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:33,3:33:899:3:45:0,-6.63712,-76.9532 +q 916 . G C 4.63106e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=3.73412;EPPR=10.2485;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=32.2266;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=855;RO=30;RPL=2;RPP=3.73412;RPPR=7.64277;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=17;SRP=4.16842;SRR=13;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:30,3:30:855:3:58:0,-4.52082,-71.7802 +q 930 . T C 1.78554e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=9.52472;EPPR=4.76149;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.6019;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=841;RO=31;RPL=3;RPP=9.52472;RPPR=3.08035;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=18;SRP=4.76149;SRR=13;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:34:31,3:31:841:3:59:0,-4.7287,-70.4186 +q 934 . T C 2.98643e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=33;DPB=33;DPRA=0;EPP=3.73412;EPPR=5.61607;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=33.1107;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=786;RO=30;RPL=2;RPP=3.73412;RPPR=3.0103;RPR=1;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=17;SRP=4.16842;SRR=13;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:33:30,3:30:786:3:59:0,-4.42767,-65.4606 +q 940 . T C 1.78476e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=9.52472;EPPR=3.08035;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=36.6019;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=945;RO=31;RPL=3;RPP=9.52472;RPPR=6.44263;RPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=18;SRP=4.76149;SRR=13;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:34:31,3:31:945:3:59:0,-4.7287,-79.7982 +q 948 . T C 1.46909e-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=45.6626;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1131;RO=34;RPL=2;RPP=7.35324;RPPR=12.2071;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=5.30951;SRR=14;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1131:2:30:0,-7.9871,-99.2046 +q 952 . T C 0 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=7.35324;EPPR=3.9754;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=48.3256;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1097;RO=36;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=20;SRP=3.9754;SRR=16;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:36,2:36:1097:2:30:0,-8.58916,-96.1236 +q 958 . T C 2.80771e-11 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=6.91895;EPPR=3.64073;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=25.7647;PAIRED=1;PAIREDR=0.967742;PAO=0;PQA=0;PQR=0;PRO=0;QA=109;QR=1021;RO=31;RPL=5;RPP=13.8677;RPPR=11.486;RPR=0;RUN=1;SAF=4;SAP=6.91895;SAR=1;SRF=16;SRP=3.08035;SRR=15;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:31,5:31:1021:5:109:0,-0.811201,-82.1297 +q 960 . T C 1.29659e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=38;DPB=38;DPRA=0;EPP=9.52472;EPPR=3.56868;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=41.3251;PAIRED=1;PAIREDR=0.971429;PAO=0;PQA=0;PQR=0;PRO=0;QA=51;QR=1022;RO=35;RPL=2;RPP=3.73412;RPPR=8.03571;RPR=1;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=19;SRP=3.56868;SRR=16;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:38:35,3:35:1022:3:51:0,-6.67921,-87.46 +q 974 . T C 1.46909e-16 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.0103;EPPR=4.03217;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=44.2763;PAIRED=1;PAIREDR=0.970588;PAO=0;PQA=0;PQR=0;PRO=0;QA=30;QR=1197;RO=34;RPL=1;RPP=3.0103;RPPR=15.5282;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=19;SRP=4.03217;SRR=15;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:36:34,2:34:1197:2:30:0,-7.9871,-105.144 diff --git a/test/fixtures/real/gencode/gencode.v50.basic.chr22.gff3 b/test/fixtures/real/gencode/gencode.v50.basic.chr22.gff3 new file mode 100644 index 0000000..900c965 --- /dev/null +++ b/test/fixtures/real/gencode/gencode.v50.basic.chr22.gff3 @@ -0,0 +1,328 @@ +##gff-version 3 +#description: evidence-based annotation of the human genome (GRCh38), version 50 (Ensembl 116) +#provider: GENCODE +#contact: gencode-help@ebi.ac.uk +#format: gff3 +#date: 2026-04-08 +##sequence-region chr1 1 248956422 +##sequence-region chr2 1 242193529 +##sequence-region chr3 1 198295559 +##sequence-region chr4 1 190214555 +##sequence-region chr5 1 181538259 +##sequence-region chr6 1 170805979 +##sequence-region chr7 1 159345973 +##sequence-region chr8 1 145138636 +##sequence-region chr9 1 138394717 +##sequence-region chr10 1 133797422 +##sequence-region chr11 1 135086622 +##sequence-region chr12 1 133275309 +##sequence-region chr13 1 114364328 +##sequence-region chr14 1 107043718 +##sequence-region chr15 1 101991189 +##sequence-region chr16 1 90338345 +##sequence-region chr17 1 83257441 +##sequence-region chr18 1 80373285 +##sequence-region chr19 1 58617616 +##sequence-region chr20 1 64444167 +##sequence-region chr21 1 46709983 +##sequence-region chr22 1 50818468 +chr22 HAVANA gene 10524345 10529164 . - . ID=ENSG00000294541.1;gene_id=ENSG00000294541.1;gene_type=lncRNA;gene_name=ENSG00000294541;level=2 +chr22 HAVANA transcript 10524345 10529164 . - . ID=ENST00000724296.1;Parent=ENSG00000294541.1;gene_id=ENSG00000294541.1;transcript_id=ENST00000724296.1;gene_type=lncRNA;gene_name=ENSG00000294541;transcript_type=lncRNA;transcript_name=ENST00000724296;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 10529036 10529164 . - . ID=exon:ENST00000724296.1:1;Parent=ENST00000724296.1;gene_id=ENSG00000294541.1;transcript_id=ENST00000724296.1;gene_type=lncRNA;gene_name=ENSG00000294541;transcript_type=lncRNA;transcript_name=ENST00000724296;exon_number=1;exon_id=ENSE00004046862.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 10527853 10528040 . - . ID=exon:ENST00000724296.1:2;Parent=ENST00000724296.1;gene_id=ENSG00000294541.1;transcript_id=ENST00000724296.1;gene_type=lncRNA;gene_name=ENSG00000294541;transcript_type=lncRNA;transcript_name=ENST00000724296;exon_number=2;exon_id=ENSE00004046860.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 10524345 10524446 . - . ID=exon:ENST00000724296.1:3;Parent=ENST00000724296.1;gene_id=ENSG00000294541.1;transcript_id=ENST00000724296.1;gene_type=lncRNA;gene_name=ENSG00000294541;transcript_type=lncRNA;transcript_name=ENST00000724296;exon_number=3;exon_id=ENSE00004046861.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 ENSEMBL gene 10736171 10736283 . - . ID=ENSG00000277248.1;gene_id=ENSG00000277248.1;gene_type=snRNA;gene_name=U2;level=3 +chr22 ENSEMBL transcript 10736171 10736283 . - . ID=ENST00000615943.1;Parent=ENSG00000277248.1;gene_id=ENSG00000277248.1;transcript_id=ENST00000615943.1;gene_type=snRNA;gene_name=U2;transcript_type=snRNA;transcript_name=U2.14-201;level=3;transcript_support_level=NA;tag=basic,Ensembl_canonical,GENCODE_Primary +chr22 ENSEMBL exon 10736171 10736283 . - . ID=exon:ENST00000615943.1:1;Parent=ENST00000615943.1;gene_id=ENSG00000277248.1;transcript_id=ENST00000615943.1;gene_type=snRNA;gene_name=U2;transcript_type=snRNA;transcript_name=U2.14-201;exon_number=1;exon_id=ENSE00003736336.1;level=3;transcript_support_level=NA;tag=basic,Ensembl_canonical,GENCODE_Primary +chr22 HAVANA gene 10742050 10753085 . + . ID=ENSG00000301473.1;gene_id=ENSG00000301473.1;gene_type=lncRNA;gene_name=ENSG00000301473;level=2 +chr22 HAVANA transcript 10742092 10753081 . + . ID=ENST00000779065.1;Parent=ENSG00000301473.1;gene_id=ENSG00000301473.1;transcript_id=ENST00000779065.1;gene_type=lncRNA;gene_name=ENSG00000301473;transcript_type=lncRNA;transcript_name=ENST00000779065;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10742092 10742191 . + . ID=exon:ENST00000779065.1:1;Parent=ENST00000779065.1;gene_id=ENSG00000301473.1;transcript_id=ENST00000779065.1;gene_type=lncRNA;gene_name=ENSG00000301473;transcript_type=lncRNA;transcript_name=ENST00000779065;exon_number=1;exon_id=ENSE00004149143.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10749498 10749658 . + . ID=exon:ENST00000779065.1:2;Parent=ENST00000779065.1;gene_id=ENSG00000301473.1;transcript_id=ENST00000779065.1;gene_type=lncRNA;gene_name=ENSG00000301473;transcript_type=lncRNA;transcript_name=ENST00000779065;exon_number=2;exon_id=ENSE00004149144.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10752760 10753081 . + . ID=exon:ENST00000779065.1:3;Parent=ENST00000779065.1;gene_id=ENSG00000301473.1;transcript_id=ENST00000779065.1;gene_type=lncRNA;gene_name=ENSG00000301473;transcript_type=lncRNA;transcript_name=ENST00000779065;exon_number=3;exon_id=ENSE00004149147.1;level=2;tag=basic,TAGENE +chr22 HAVANA gene 10752636 10754413 . - . ID=ENSG00000301496.1;gene_id=ENSG00000301496.1;gene_type=lncRNA;gene_name=ENSG00000301496;level=2 +chr22 HAVANA transcript 10752636 10754413 . - . ID=ENST00000779294.1;Parent=ENSG00000301496.1;gene_id=ENSG00000301496.1;transcript_id=ENST00000779294.1;gene_type=lncRNA;gene_name=ENSG00000301496;transcript_type=lncRNA;transcript_name=ENST00000779294;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 10754322 10754413 . - . ID=exon:ENST00000779294.1:1;Parent=ENST00000779294.1;gene_id=ENSG00000301496.1;transcript_id=ENST00000779294.1;gene_type=lncRNA;gene_name=ENSG00000301496;transcript_type=lncRNA;transcript_name=ENST00000779294;exon_number=1;exon_id=ENSE00004149605.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 10752636 10752913 . - . ID=exon:ENST00000779294.1:2;Parent=ENST00000779294.1;gene_id=ENSG00000301496.1;transcript_id=ENST00000779294.1;gene_type=lncRNA;gene_name=ENSG00000301496;transcript_type=lncRNA;transcript_name=ENST00000779294;exon_number=2;exon_id=ENSE00004149606.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA gene 10939388 10961338 . - . ID=ENSG00000283047.1;gene_id=ENSG00000283047.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;level=2;hgnc_id=HGNC:51765;tag=overlapping_locus;havana_gene=OTTHUMG00000191577.1 +chr22 HAVANA transcript 10939388 10961338 . - . ID=ENST00000635667.1;Parent=ENSG00000283047.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10961283 10961338 . - . ID=exon:ENST00000635667.1:1;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=1;exon_id=ENSE00003786612.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10959067 10959136 . - . ID=exon:ENST00000635667.1:2;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=2;exon_id=ENSE00003789146.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10950049 10950174 . - . ID=exon:ENST00000635667.1:3;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=3;exon_id=ENSE00003786193.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10949212 10949269 . - . ID=exon:ENST00000635667.1:4;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=4;exon_id=ENSE00003784997.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10947304 10947418 . - . ID=exon:ENST00000635667.1:5;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=5;exon_id=ENSE00003787541.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10944967 10945053 . - . ID=exon:ENST00000635667.1:6;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=6;exon_id=ENSE00003785466.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10941691 10941780 . - . ID=exon:ENST00000635667.1:7;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=7;exon_id=ENSE00003787209.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10940597 10940707 . - . ID=exon:ENST00000635667.1:8;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=8;exon_id=ENSE00003791492.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA exon 10939388 10939423 . - . ID=exon:ENST00000635667.1:9;Parent=ENST00000635667.1;gene_id=ENSG00000283047.1;transcript_id=ENST00000635667.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=FRG1FP;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=FRG1FP-201;exon_number=9;exon_id=ENSE00003790077.1;level=2;transcript_support_level=NA;hgnc_id=HGNC:51765;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000191577.1;havana_transcript=OTTHUMT00000488611.1 +chr22 HAVANA gene 10941695 10961693 . - . ID=ENSG00000303605.1;gene_id=ENSG00000303605.1;gene_type=lncRNA;gene_name=ENSG00000303605;level=2;tag=overlapping_locus,overlaps_pseudogene +chr22 HAVANA transcript 10941695 10961556 . - . ID=ENST00000796039.1;Parent=ENSG00000303605.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10960994 10961556 . - . ID=exon:ENST00000796039.1:1;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=1;exon_id=ENSE00004181266.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10960278 10960431 . - . ID=exon:ENST00000796039.1:2;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=2;exon_id=ENSE00004181253.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10959067 10959136 . - . ID=exon:ENST00000796039.1:3;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=3;exon_id=ENSE00004181258.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10950049 10950174 . - . ID=exon:ENST00000796039.1:4;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=4;exon_id=ENSE00004181255.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10949212 10949269 . - . ID=exon:ENST00000796039.1:5;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=5;exon_id=ENSE00004181254.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10947304 10947418 . - . ID=exon:ENST00000796039.1:6;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=6;exon_id=ENSE00004181267.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10944967 10945053 . - . ID=exon:ENST00000796039.1:7;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=7;exon_id=ENSE00004181264.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10941695 10941780 . - . ID=exon:ENST00000796039.1:8;Parent=ENST00000796039.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796039.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796039;exon_number=8;exon_id=ENSE00004181259.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 10944590 10961586 . - . ID=ENST00000796042.1;Parent=ENSG00000303605.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10961283 10961586 . - . ID=exon:ENST00000796042.1:1;Parent=ENST00000796042.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;exon_number=1;exon_id=ENSE00004181257.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10960332 10960514 . - . ID=exon:ENST00000796042.1:2;Parent=ENST00000796042.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;exon_number=2;exon_id=ENSE00004181260.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10959067 10959136 . - . ID=exon:ENST00000796042.1:3;Parent=ENST00000796042.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;exon_number=3;exon_id=ENSE00004181258.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10950049 10950174 . - . ID=exon:ENST00000796042.1:4;Parent=ENST00000796042.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;exon_number=4;exon_id=ENSE00004181255.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10949212 10949269 . - . ID=exon:ENST00000796042.1:5;Parent=ENST00000796042.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;exon_number=5;exon_id=ENSE00004181254.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10947304 10947418 . - . ID=exon:ENST00000796042.1:6;Parent=ENST00000796042.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;exon_number=6;exon_id=ENSE00004181267.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 10944590 10945053 . - . ID=exon:ENST00000796042.1:7;Parent=ENST00000796042.1;gene_id=ENSG00000303605.1;transcript_id=ENST00000796042.1;gene_type=lncRNA;gene_name=ENSG00000303605;transcript_type=lncRNA;transcript_name=ENST00000796042;exon_number=7;exon_id=ENSE00004181265.1;level=2;tag=basic,TAGENE +chr22 HAVANA gene 11066268 11068174 . + . ID=ENSG00000279973.3;gene_id=ENSG00000279973.3;gene_type=lncRNA;gene_name=ENSG00000279973;level=2;havana_gene=OTTHUMG00000192006.1 +chr22 HAVANA transcript 11066268 11068174 . + . ID=ENST00000624155.3;Parent=ENSG00000279973.3;gene_id=ENSG00000279973.3;transcript_id=ENST00000624155.3;gene_type=lncRNA;gene_name=ENSG00000279973;transcript_type=lncRNA;transcript_name=ENST00000624155;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE;havana_gene=OTTHUMG00000192006.1;havana_transcript=OTTHUMT00000491988.1 +chr22 HAVANA exon 11066268 11066515 . + . ID=exon:ENST00000624155.3:1;Parent=ENST00000624155.3;gene_id=ENSG00000279973.3;transcript_id=ENST00000624155.3;gene_type=lncRNA;gene_name=ENSG00000279973;transcript_type=lncRNA;transcript_name=ENST00000624155;exon_number=1;exon_id=ENSE00004077563.1;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE;havana_gene=OTTHUMG00000192006.1;havana_transcript=OTTHUMT00000491988.1 +chr22 HAVANA exon 11067985 11068174 . + . ID=exon:ENST00000624155.3:2;Parent=ENST00000624155.3;gene_id=ENSG00000279973.3;transcript_id=ENST00000624155.3;gene_type=lncRNA;gene_name=ENSG00000279973;transcript_type=lncRNA;transcript_name=ENST00000624155;exon_number=2;exon_id=ENSE00003758861.2;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE;havana_gene=OTTHUMG00000192006.1;havana_transcript=OTTHUMT00000491988.1 +chr22 HAVANA gene 11124337 11125705 . + . ID=ENSG00000226444.2;gene_id=ENSG00000226444.2;gene_type=processed_pseudogene;gene_name=ACTR3BP7;level=1;hgnc_id=HGNC:54971;tag=pseudo_consens;havana_gene=OTTHUMG00000140398.2 +chr22 HAVANA transcript 11124337 11125705 . + . ID=ENST00000422332.1;Parent=ENSG00000226444.2;gene_id=ENSG00000226444.2;transcript_id=ENST00000422332.1;gene_type=processed_pseudogene;gene_name=ACTR3BP7;transcript_type=processed_pseudogene;transcript_name=ACTR3BP7-201;level=1;transcript_support_level=NA;hgnc_id=HGNC:54971;ont=PGO:0000004;tag=pseudo_consens,basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000140398.2;havana_transcript=OTTHUMT00000277200.2 +chr22 HAVANA exon 11124337 11124379 . + . ID=exon:ENST00000422332.1:1;Parent=ENST00000422332.1;gene_id=ENSG00000226444.2;transcript_id=ENST00000422332.1;gene_type=processed_pseudogene;gene_name=ACTR3BP7;transcript_type=processed_pseudogene;transcript_name=ACTR3BP7-201;exon_number=1;exon_id=ENSE00001616995.1;level=1;transcript_support_level=NA;hgnc_id=HGNC:54971;ont=PGO:0000004;tag=pseudo_consens,basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000140398.2;havana_transcript=OTTHUMT00000277200.2 +chr22 HAVANA exon 11124508 11125705 . + . ID=exon:ENST00000422332.1:2;Parent=ENST00000422332.1;gene_id=ENSG00000226444.2;transcript_id=ENST00000422332.1;gene_type=processed_pseudogene;gene_name=ACTR3BP7;transcript_type=processed_pseudogene;transcript_name=ACTR3BP7-201;exon_number=2;exon_id=ENSE00001776473.1;level=1;transcript_support_level=NA;hgnc_id=HGNC:54971;ont=PGO:0000004;tag=pseudo_consens,basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000140398.2;havana_transcript=OTTHUMT00000277200.2 +chr22 HAVANA gene 11146119 11147823 . + . ID=ENSG00000294022.1;gene_id=ENSG00000294022.1;gene_type=lncRNA;gene_name=ENSG00000294022;level=2 +chr22 HAVANA transcript 11146119 11147823 . + . ID=ENST00000720620.1;Parent=ENSG00000294022.1;gene_id=ENSG00000294022.1;transcript_id=ENST00000720620.1;gene_type=lncRNA;gene_name=ENSG00000294022;transcript_type=lncRNA;transcript_name=ENST00000720620;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 11146119 11146180 . + . ID=exon:ENST00000720620.1:1;Parent=ENST00000720620.1;gene_id=ENSG00000294022.1;transcript_id=ENST00000720620.1;gene_type=lncRNA;gene_name=ENSG00000294022;transcript_type=lncRNA;transcript_name=ENST00000720620;exon_number=1;exon_id=ENSE00004039547.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 11146349 11146429 . + . ID=exon:ENST00000720620.1:2;Parent=ENST00000720620.1;gene_id=ENSG00000294022.1;transcript_id=ENST00000720620.1;gene_type=lncRNA;gene_name=ENSG00000294022;transcript_type=lncRNA;transcript_name=ENST00000720620;exon_number=2;exon_id=ENSE00004039545.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 11147580 11147823 . + . ID=exon:ENST00000720620.1:3;Parent=ENST00000720620.1;gene_id=ENSG00000294022.1;transcript_id=ENST00000720620.1;gene_type=lncRNA;gene_name=ENSG00000294022;transcript_type=lncRNA;transcript_name=ENST00000720620;exon_number=3;exon_id=ENSE00004039546.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 ENSEMBL gene 11249809 11249959 . - . ID=ENSG00000276871.1;gene_id=ENSG00000276871.1;gene_type=rRNA;gene_name=5_8S_rRNA;level=3 +chr22 ENSEMBL transcript 11249809 11249959 . - . ID=ENST00000612732.1;Parent=ENSG00000276871.1;gene_id=ENSG00000276871.1;transcript_id=ENST00000612732.1;gene_type=rRNA;gene_name=5_8S_rRNA;transcript_type=rRNA;transcript_name=5_8S_rRNA.4-201;level=3;transcript_support_level=NA;tag=basic,Ensembl_canonical,GENCODE_Primary +chr22 ENSEMBL exon 11249809 11249959 . - . ID=exon:ENST00000612732.1:1;Parent=ENST00000612732.1;gene_id=ENSG00000276871.1;transcript_id=ENST00000612732.1;gene_type=rRNA;gene_name=5_8S_rRNA;transcript_type=rRNA;transcript_name=5_8S_rRNA.4-201;exon_number=1;exon_id=ENSE00003735240.1;level=3;transcript_support_level=NA;tag=basic,Ensembl_canonical,GENCODE_Primary +chr22 HAVANA gene 11474744 11479643 . + . ID=ENSG00000288262.1;gene_id=ENSG00000288262.1;gene_type=unprocessed_pseudogene;gene_name=ZNF73P;level=2;hgnc_id=HGNC:13143;havana_gene=OTTHUMG00000195920.1 +chr22 HAVANA transcript 11474744 11479643 . + . ID=ENST00000672261.1;Parent=ENSG00000288262.1;gene_id=ENSG00000288262.1;transcript_id=ENST00000672261.1;gene_type=unprocessed_pseudogene;gene_name=ZNF73P;transcript_type=unprocessed_pseudogene;transcript_name=ZNF73P-201;level=2;hgnc_id=HGNC:13143;ont=PGO:0000005;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000195920.1;havana_transcript=OTTHUMT00000529609.1 +chr22 HAVANA exon 11474744 11474904 . + . ID=exon:ENST00000672261.1:1;Parent=ENST00000672261.1;gene_id=ENSG00000288262.1;transcript_id=ENST00000672261.1;gene_type=unprocessed_pseudogene;gene_name=ZNF73P;transcript_type=unprocessed_pseudogene;transcript_name=ZNF73P-201;exon_number=1;exon_id=ENSE00003893399.1;level=2;hgnc_id=HGNC:13143;ont=PGO:0000005;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000195920.1;havana_transcript=OTTHUMT00000529609.1 +chr22 HAVANA exon 11475146 11475238 . + . ID=exon:ENST00000672261.1:2;Parent=ENST00000672261.1;gene_id=ENSG00000288262.1;transcript_id=ENST00000672261.1;gene_type=unprocessed_pseudogene;gene_name=ZNF73P;transcript_type=unprocessed_pseudogene;transcript_name=ZNF73P-201;exon_number=2;exon_id=ENSE00003891926.1;level=2;hgnc_id=HGNC:13143;ont=PGO:0000005;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000195920.1;havana_transcript=OTTHUMT00000529609.1 +chr22 HAVANA exon 11477178 11479643 . + . ID=exon:ENST00000672261.1:3;Parent=ENST00000672261.1;gene_id=ENSG00000288262.1;transcript_id=ENST00000672261.1;gene_type=unprocessed_pseudogene;gene_name=ZNF73P;transcript_type=unprocessed_pseudogene;transcript_name=ZNF73P-201;exon_number=3;exon_id=ENSE00003892093.1;level=2;hgnc_id=HGNC:13143;ont=PGO:0000005;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000195920.1;havana_transcript=OTTHUMT00000529609.1 +chr22 HAVANA gene 11707145 11955470 . + . ID=ENSG00000290397.2;gene_id=ENSG00000290397.2;gene_type=lncRNA;gene_name=ENSG00000290397;level=2;tag=overlaps_pseudogene +chr22 HAVANA transcript 11707176 11886438 . + . ID=ENST00000849404.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11707176 11707423 . + . ID=exon:ENST00000849404.1:1;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=1;exon_id=ENSE00004279894.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11832761 11832915 . + . ID=exon:ENST00000849404.1:2;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=2;exon_id=ENSE00003884543.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11867115 11867145 . + . ID=exon:ENST00000849404.1:3;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=3;exon_id=ENSE00003864175.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11869829 11869898 . + . ID=exon:ENST00000849404.1:4;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=4;exon_id=ENSE00003886323.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11870756 11870787 . + . ID=exon:ENST00000849404.1:5;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=5;exon_id=ENSE00004279888.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11873841 11873925 . + . ID=exon:ENST00000849404.1:6;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=6;exon_id=ENSE00003876297.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876104 11876132 . + . ID=exon:ENST00000849404.1:7;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=7;exon_id=ENSE00003884551.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876224 11876296 . + . ID=exon:ENST00000849404.1:8;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=8;exon_id=ENSE00003880389.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11882268 11882338 . + . ID=exon:ENST00000849404.1:9;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=9;exon_id=ENSE00003877785.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11886401 11886438 . + . ID=exon:ENST00000849404.1:10;Parent=ENST00000849404.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849404.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849404;exon_number=10;exon_id=ENSE00004279874.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11707179 11869574 . + . ID=ENST00000849410.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849410.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849410;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11707179 11707423 . + . ID=exon:ENST00000849410.1:1;Parent=ENST00000849410.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849410.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849410;exon_number=1;exon_id=ENSE00004279876.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11832761 11832915 . + . ID=exon:ENST00000849410.1:2;Parent=ENST00000849410.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849410.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849410;exon_number=2;exon_id=ENSE00003884543.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11867115 11869574 . + . ID=exon:ENST00000849410.1:3;Parent=ENST00000849410.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849410.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849410;exon_number=3;exon_id=ENSE00004279870.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11709407 11715712 . + . ID=ENST00000849442.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849442.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849442;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11709407 11709542 . + . ID=exon:ENST00000849442.1:1;Parent=ENST00000849442.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849442.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849442;exon_number=1;exon_id=ENSE00004279908.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11714674 11715712 . + . ID=exon:ENST00000849442.1:2;Parent=ENST00000849442.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849442.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849442;exon_number=2;exon_id=ENSE00004279903.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11825264 11833819 . + . ID=ENST00000849438.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849438.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849438;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11825264 11825547 . + . ID=exon:ENST00000849438.1:1;Parent=ENST00000849438.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849438.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849438;exon_number=1;exon_id=ENSE00004279895.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11832761 11833819 . + . ID=exon:ENST00000849438.1:2;Parent=ENST00000849438.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849438.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849438;exon_number=2;exon_id=ENSE00004279887.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11827522 11889435 . + . ID=ENST00000849415.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11827522 11827658 . + . ID=exon:ENST00000849415.1:1;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=1;exon_id=ENSE00004279914.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11832761 11832915 . + . ID=exon:ENST00000849415.1:2;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=2;exon_id=ENSE00003884543.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11873844 11873925 . + . ID=exon:ENST00000849415.1:3;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=3;exon_id=ENSE00004279875.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876104 11876132 . + . ID=exon:ENST00000849415.1:4;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=4;exon_id=ENSE00003884551.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876224 11876296 . + . ID=exon:ENST00000849415.1:5;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=5;exon_id=ENSE00003880389.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11882268 11882338 . + . ID=exon:ENST00000849415.1:6;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=6;exon_id=ENSE00003877785.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11886401 11886565 . + . ID=exon:ENST00000849415.1:7;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=7;exon_id=ENSE00004811648.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11887952 11888146 . + . ID=exon:ENST00000849415.1:8;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=8;exon_id=ENSE00004279873.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11889310 11889435 . + . ID=exon:ENST00000849415.1:9;Parent=ENST00000849415.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849415.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849415;exon_number=9;exon_id=ENSE00004279905.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11827522 11910358 . + . ID=ENST00000657566.2;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11827522 11827658 . + . ID=exon:ENST00000657566.2:1;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=1;exon_id=ENSE00004279914.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11832761 11832915 . + . ID=exon:ENST00000657566.2:2;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=2;exon_id=ENSE00003884543.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11867115 11867145 . + . ID=exon:ENST00000657566.2:3;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=3;exon_id=ENSE00003864175.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11869829 11869898 . + . ID=exon:ENST00000657566.2:4;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=4;exon_id=ENSE00003886323.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11872163 11872354 . + . ID=exon:ENST00000657566.2:5;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=5;exon_id=ENSE00003874242.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11873841 11873925 . + . ID=exon:ENST00000657566.2:6;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=6;exon_id=ENSE00003876297.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11876104 11876132 . + . ID=exon:ENST00000657566.2:7;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=7;exon_id=ENSE00003884551.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11876224 11876296 . + . ID=exon:ENST00000657566.2:8;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=8;exon_id=ENSE00003880389.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11882268 11882338 . + . ID=exon:ENST00000657566.2:9;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=9;exon_id=ENSE00003877785.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11886401 11886565 . + . ID=exon:ENST00000657566.2:10;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=10;exon_id=ENSE00004811648.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11887952 11888146 . + . ID=exon:ENST00000657566.2:11;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=11;exon_id=ENSE00004279873.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11889310 11890230 . + . ID=exon:ENST00000657566.2:12;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=12;exon_id=ENSE00004811640.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11891782 11891931 . + . ID=exon:ENST00000657566.2:13;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=13;exon_id=ENSE00004811641.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11902861 11903142 . + . ID=exon:ENST00000657566.2:14;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=14;exon_id=ENSE00004811643.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11903787 11904000 . + . ID=exon:ENST00000657566.2:15;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=15;exon_id=ENSE00004811645.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11905337 11905557 . + . ID=exon:ENST00000657566.2:16;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=16;exon_id=ENSE00003885180.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA exon 11910166 11910358 . + . ID=exon:ENST00000657566.2:17;Parent=ENST00000657566.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000657566.2;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000657566;exon_number=17;exon_id=ENSE00003868543.1;level=2;tag=RNA_Seq_supported_only,basic,TAGENE;havana_transcript=OTTHUMT00000504859.1 +chr22 HAVANA transcript 11827523 11870977 . + . ID=ENST00000849423.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849423.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849423;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11827523 11827658 . + . ID=exon:ENST00000849423.1:1;Parent=ENST00000849423.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849423.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849423;exon_number=1;exon_id=ENSE00004279921.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11832761 11832915 . + . ID=exon:ENST00000849423.1:2;Parent=ENST00000849423.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849423.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849423;exon_number=2;exon_id=ENSE00003884543.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11867115 11867145 . + . ID=exon:ENST00000849423.1:3;Parent=ENST00000849423.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849423.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849423;exon_number=3;exon_id=ENSE00003864175.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11869054 11869125 . + . ID=exon:ENST00000849423.1:4;Parent=ENST00000849423.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849423.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849423;exon_number=4;exon_id=ENSE00004279896.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11869829 11870977 . + . ID=exon:ENST00000849423.1:5;Parent=ENST00000849423.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849423.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849423;exon_number=5;exon_id=ENSE00004279907.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11859802 11889426 . + . ID=ENST00000849431.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11859802 11859927 . + . ID=exon:ENST00000849431.1:1;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=1;exon_id=ENSE00004279872.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11867115 11867145 . + . ID=exon:ENST00000849431.1:2;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=2;exon_id=ENSE00003864175.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11869829 11869898 . + . ID=exon:ENST00000849431.1:3;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=3;exon_id=ENSE00003886323.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11872163 11872358 . + . ID=exon:ENST00000849431.1:4;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=4;exon_id=ENSE00004279884.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11873841 11873925 . + . ID=exon:ENST00000849431.1:5;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=5;exon_id=ENSE00003876297.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876104 11876132 . + . ID=exon:ENST00000849431.1:6;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=6;exon_id=ENSE00003884551.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876224 11876296 . + . ID=exon:ENST00000849431.1:7;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=7;exon_id=ENSE00003880389.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11882268 11882338 . + . ID=exon:ENST00000849431.1:8;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=8;exon_id=ENSE00003877785.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11886401 11886565 . + . ID=exon:ENST00000849431.1:9;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=9;exon_id=ENSE00004811648.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11887952 11888146 . + . ID=exon:ENST00000849431.1:10;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=10;exon_id=ENSE00004279873.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11889310 11889426 . + . ID=exon:ENST00000849431.1:11;Parent=ENST00000849431.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849431.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849431;exon_number=11;exon_id=ENSE00004279891.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11859817 11890645 . + . ID=ENST00000849426.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11859817 11859927 . + . ID=exon:ENST00000849426.1:1;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=1;exon_id=ENSE00004279878.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11867115 11867145 . + . ID=exon:ENST00000849426.1:2;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=2;exon_id=ENSE00003864175.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11869054 11869125 . + . ID=exon:ENST00000849426.1:3;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=3;exon_id=ENSE00004279896.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11869829 11869898 . + . ID=exon:ENST00000849426.1:4;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=4;exon_id=ENSE00003886323.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11872163 11872354 . + . ID=exon:ENST00000849426.1:5;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=5;exon_id=ENSE00003874242.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11873844 11873925 . + . ID=exon:ENST00000849426.1:6;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=6;exon_id=ENSE00004279875.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876104 11876132 . + . ID=exon:ENST00000849426.1:7;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=7;exon_id=ENSE00003884551.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876224 11876296 . + . ID=exon:ENST00000849426.1:8;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=8;exon_id=ENSE00003880389.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11881986 11882119 . + . ID=exon:ENST00000849426.1:9;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=9;exon_id=ENSE00004279918.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11882268 11882338 . + . ID=exon:ENST00000849426.1:10;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=10;exon_id=ENSE00003877785.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11886401 11886565 . + . ID=exon:ENST00000849426.1:11;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=11;exon_id=ENSE00004811648.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11887952 11888146 . + . ID=exon:ENST00000849426.1:12;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=12;exon_id=ENSE00004279873.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11889310 11890645 . + . ID=exon:ENST00000849426.1:13;Parent=ENST00000849426.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849426.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849426;exon_number=13;exon_id=ENSE00004279932.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11859827 11889925 . + . ID=ENST00000849428.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11859827 11859927 . + . ID=exon:ENST00000849428.1:1;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=1;exon_id=ENSE00004279925.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11867115 11867145 . + . ID=exon:ENST00000849428.1:2;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=2;exon_id=ENSE00003864175.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11869829 11869898 . + . ID=exon:ENST00000849428.1:3;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=3;exon_id=ENSE00003886323.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11873841 11873925 . + . ID=exon:ENST00000849428.1:4;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=4;exon_id=ENSE00003876297.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876104 11876132 . + . ID=exon:ENST00000849428.1:5;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=5;exon_id=ENSE00003884551.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11876224 11876296 . + . ID=exon:ENST00000849428.1:6;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=6;exon_id=ENSE00003880389.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11882268 11882338 . + . ID=exon:ENST00000849428.1:7;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=7;exon_id=ENSE00003877785.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11886401 11886565 . + . ID=exon:ENST00000849428.1:8;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=8;exon_id=ENSE00004811648.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11887952 11888146 . + . ID=exon:ENST00000849428.1:9;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=9;exon_id=ENSE00004279873.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11889310 11889925 . + . ID=exon:ENST00000849428.1:10;Parent=ENST00000849428.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849428.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849428;exon_number=10;exon_id=ENSE00004279917.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11897376 11915770 . + . ID=ENST00000849433.1;Parent=ENSG00000290397.2;gene_id=ENSG00000290397.2;transcript_id=ENST00000849433.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849433;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11897376 11897467 . + . ID=exon:ENST00000849433.1:1;Parent=ENST00000849433.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849433.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849433;exon_number=1;exon_id=ENSE00004279885.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11910166 11910219 . + . ID=exon:ENST00000849433.1:2;Parent=ENST00000849433.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849433.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849433;exon_number=2;exon_id=ENSE00004279897.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11913040 11913192 . + . ID=exon:ENST00000849433.1:3;Parent=ENST00000849433.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849433.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849433;exon_number=3;exon_id=ENSE00004279916.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11914501 11915770 . + . ID=exon:ENST00000849433.1:4;Parent=ENST00000849433.1;gene_id=ENSG00000290397.2;transcript_id=ENST00000849433.1;gene_type=lncRNA;gene_name=ENSG00000290397;transcript_type=lncRNA;transcript_name=ENST00000849433;exon_number=4;exon_id=ENSE00004279913.1;level=2;tag=basic,TAGENE +chr22 HAVANA gene 11832287 11974294 . - . ID=ENSG00000310416.1;gene_id=ENSG00000310416.1;gene_type=lncRNA;gene_name=ENSG00000310416;level=2 +chr22 HAVANA transcript 11832621 11974223 . - . ID=ENST00000849584.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849584.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849584;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11974138 11974223 . - . ID=exon:ENST00000849584.1:1;Parent=ENST00000849584.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849584.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849584;exon_number=1;exon_id=ENSE00004280383.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11973415 11973633 . - . ID=exon:ENST00000849584.1:2;Parent=ENST00000849584.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849584.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849584;exon_number=2;exon_id=ENSE00004280322.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849584.1:3;Parent=ENST00000849584.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849584.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849584;exon_number=3;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11868679 11868961 . - . ID=exon:ENST00000849584.1:4;Parent=ENST00000849584.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849584.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849584;exon_number=4;exon_id=ENSE00004280275.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11846227 11846349 . - . ID=exon:ENST00000849584.1:5;Parent=ENST00000849584.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849584.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849584;exon_number=5;exon_id=ENSE00004280308.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11832621 11832954 . - . ID=exon:ENST00000849584.1:6;Parent=ENST00000849584.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849584.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849584;exon_number=6;exon_id=ENSE00004280351.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11833182 11974184 . - . ID=ENST00000849596.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849596.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849596;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11974015 11974184 . - . ID=exon:ENST00000849596.1:1;Parent=ENST00000849596.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849596.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849596;exon_number=1;exon_id=ENSE00004280387.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11973277 11973364 . - . ID=exon:ENST00000849596.1:2;Parent=ENST00000849596.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849596.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849596;exon_number=2;exon_id=ENSE00004280295.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849596.1:3;Parent=ENST00000849596.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849596.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849596;exon_number=3;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11846227 11846349 . - . ID=exon:ENST00000849596.1:4;Parent=ENST00000849596.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849596.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849596;exon_number=4;exon_id=ENSE00004280308.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11833182 11833801 . - . ID=exon:ENST00000849596.1:5;Parent=ENST00000849596.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849596.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849596;exon_number=5;exon_id=ENSE00004280310.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11843099 11974198 . - . ID=ENST00000849602.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11974015 11974198 . - . ID=exon:ENST00000849602.1:1;Parent=ENST00000849602.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;exon_number=1;exon_id=ENSE00004280342.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849602.1:2;Parent=ENST00000849602.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;exon_number=2;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11878920 11879007 . - . ID=exon:ENST00000849602.1:3;Parent=ENST00000849602.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;exon_number=3;exon_id=ENSE00004280373.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11868679 11868961 . - . ID=exon:ENST00000849602.1:4;Parent=ENST00000849602.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;exon_number=4;exon_id=ENSE00004280275.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11846227 11846349 . - . ID=exon:ENST00000849602.1:5;Parent=ENST00000849602.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;exon_number=5;exon_id=ENSE00004280308.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11845698 11845742 . - . ID=exon:ENST00000849602.1:6;Parent=ENST00000849602.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;exon_number=6;exon_id=ENSE00004280312.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11843099 11844371 . - . ID=exon:ENST00000849602.1:7;Parent=ENST00000849602.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849602.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849602;exon_number=7;exon_id=ENSE00004280278.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11849156 11974214 . - . ID=ENST00000849617.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849617.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849617;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11974138 11974214 . - . ID=exon:ENST00000849617.1:1;Parent=ENST00000849617.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849617.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849617;exon_number=1;exon_id=ENSE00004280375.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849617.1:2;Parent=ENST00000849617.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849617.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849617;exon_number=2;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11967956 11968015 . - . ID=exon:ENST00000849617.1:3;Parent=ENST00000849617.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849617.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849617;exon_number=3;exon_id=ENSE00004280354.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11868679 11868946 . - . ID=exon:ENST00000849617.1:4;Parent=ENST00000849617.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849617.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849617;exon_number=4;exon_id=ENSE00004280360.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11849156 11849410 . - . ID=exon:ENST00000849617.1:5;Parent=ENST00000849617.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849617.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849617;exon_number=5;exon_id=ENSE00004280371.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11909005 11974189 . - . ID=ENST00000849633.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849633.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849633;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11973415 11974189 . - . ID=exon:ENST00000849633.1:1;Parent=ENST00000849633.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849633.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849633;exon_number=1;exon_id=ENSE00004280293.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849633.1:2;Parent=ENST00000849633.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849633.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849633;exon_number=2;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11910629 11910824 . - . ID=exon:ENST00000849633.1:3;Parent=ENST00000849633.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849633.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849633;exon_number=3;exon_id=ENSE00004280299.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11909005 11910230 . - . ID=exon:ENST00000849633.1:4;Parent=ENST00000849633.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849633.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849633;exon_number=4;exon_id=ENSE00004280355.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11910581 11974223 . - . ID=ENST00000849636.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849636.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849636;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11973931 11974223 . - . ID=exon:ENST00000849636.1:1;Parent=ENST00000849636.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849636.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849636;exon_number=1;exon_id=ENSE00004280305.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849636.1:2;Parent=ENST00000849636.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849636.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849636;exon_number=2;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11925034 11925073 . - . ID=exon:ENST00000849636.1:3;Parent=ENST00000849636.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849636.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849636;exon_number=3;exon_id=ENSE00004280384.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11912216 11912317 . - . ID=exon:ENST00000849636.1:4;Parent=ENST00000849636.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849636.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849636;exon_number=4;exon_id=ENSE00004280377.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11910581 11911026 . - . ID=exon:ENST00000849636.1:5;Parent=ENST00000849636.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849636.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849636;exon_number=5;exon_id=ENSE00004280376.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11925292 11974155 . - . ID=ENST00000849642.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849642.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849642;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11973931 11974155 . - . ID=exon:ENST00000849642.1:1;Parent=ENST00000849642.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849642.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849642;exon_number=1;exon_id=ENSE00004280349.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849642.1:2;Parent=ENST00000849642.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849642.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849642;exon_number=2;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11928542 11929140 . - . ID=exon:ENST00000849642.1:3;Parent=ENST00000849642.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849642.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849642;exon_number=3;exon_id=ENSE00004280343.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11925292 11926287 . - . ID=exon:ENST00000849642.1:4;Parent=ENST00000849642.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849642.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849642;exon_number=4;exon_id=ENSE00004280277.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 11928502 11974185 . - . ID=ENST00000849650.1;Parent=ENSG00000310416.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849650.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849650;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11974015 11974185 . - . ID=exon:ENST00000849650.1:1;Parent=ENST00000849650.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849650.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849650;exon_number=1;exon_id=ENSE00004280331.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11973415 11973607 . - . ID=exon:ENST00000849650.1:2;Parent=ENST00000849650.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849650.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849650;exon_number=2;exon_id=ENSE00004280276.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11971940 11971998 . - . ID=exon:ENST00000849650.1:3;Parent=ENST00000849650.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849650.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849650;exon_number=3;exon_id=ENSE00004280282.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 11928502 11929140 . - . ID=exon:ENST00000849650.1:4;Parent=ENST00000849650.1;gene_id=ENSG00000310416.1;transcript_id=ENST00000849650.1;gene_type=lncRNA;gene_name=ENSG00000310416;transcript_type=lncRNA;transcript_name=ENST00000849650;exon_number=4;exon_id=ENSE00004280352.1;level=2;tag=basic,TAGENE +chr22 HAVANA gene 11883602 11904000 . + . ID=ENSG00000286406.2;gene_id=ENSG00000286406.2;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;level=2;havana_gene=OTTHUMG00000193804.1 +chr22 HAVANA transcript 11883602 11904000 . + . ID=ENST00000657645.1;Parent=ENSG00000286406.2;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA exon 11883602 11884628 . + . ID=exon:ENST00000657645.1:1;Parent=ENST00000657645.1;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;exon_number=1;exon_id=ENSE00003871741.1;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA exon 11886401 11886565 . + . ID=exon:ENST00000657645.1:2;Parent=ENST00000657645.1;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;exon_number=2;exon_id=ENSE00003869821.1;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA exon 11887952 11888146 . + . ID=exon:ENST00000657645.1:3;Parent=ENST00000657645.1;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;exon_number=3;exon_id=ENSE00003858885.1;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA exon 11889310 11890230 . + . ID=exon:ENST00000657645.1:4;Parent=ENST00000657645.1;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;exon_number=4;exon_id=ENSE00003859113.1;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA exon 11891782 11891931 . + . ID=exon:ENST00000657645.1:5;Parent=ENST00000657645.1;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;exon_number=5;exon_id=ENSE00003859245.1;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA exon 11902861 11903142 . + . ID=exon:ENST00000657645.1:6;Parent=ENST00000657645.1;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;exon_number=6;exon_id=ENSE00003861322.1;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA exon 11903787 11904000 . + . ID=exon:ENST00000657645.1:7;Parent=ENST00000657645.1;gene_id=ENSG00000286406.2;transcript_id=ENST00000657645.1;gene_type=transcribed_unprocessed_pseudogene;gene_name=ENSG00000286406;transcript_type=transcribed_unprocessed_pseudogene;transcript_name=ENST00000657645;exon_number=7;exon_id=ENSE00003862233.1;level=2;ont=PGO:0000005,PGO:0000019;tag=basic,Ensembl_canonical,GENCODE_Primary;havana_gene=OTTHUMG00000193804.1;havana_transcript=OTTHUMT00000504860.1 +chr22 HAVANA gene 12038112 12056544 . - . ID=ENSG00000296155.1;gene_id=ENSG00000296155.1;gene_type=lncRNA;gene_name=ENSG00000296155;level=2 +chr22 HAVANA transcript 12038112 12056544 . - . ID=ENST00000736916.1;Parent=ENSG00000296155.1;gene_id=ENSG00000296155.1;transcript_id=ENST00000736916.1;gene_type=lncRNA;gene_name=ENSG00000296155;transcript_type=lncRNA;transcript_name=ENST00000736916;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12056492 12056544 . - . ID=exon:ENST00000736916.1:1;Parent=ENST00000736916.1;gene_id=ENSG00000296155.1;transcript_id=ENST00000736916.1;gene_type=lncRNA;gene_name=ENSG00000296155;transcript_type=lncRNA;transcript_name=ENST00000736916;exon_number=1;exon_id=ENSE00004070662.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12038112 12038831 . - . ID=exon:ENST00000736916.1:2;Parent=ENST00000736916.1;gene_id=ENSG00000296155.1;transcript_id=ENST00000736916.1;gene_type=lncRNA;gene_name=ENSG00000296155;transcript_type=lncRNA;transcript_name=ENST00000736916;exon_number=2;exon_id=ENSE00004070665.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA gene 12097900 12219507 . + . ID=ENSG00000298316.1;gene_id=ENSG00000298316.1;gene_type=lncRNA;gene_name=ENSG00000298316;level=2 +chr22 HAVANA transcript 12097902 12116171 . + . ID=ENST00000754841.1;Parent=ENSG00000298316.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754841.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754841;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12097902 12098112 . + . ID=exon:ENST00000754841.1:1;Parent=ENST00000754841.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754841.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754841;exon_number=1;exon_id=ENSE00004103176.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12100134 12100192 . + . ID=exon:ENST00000754841.1:2;Parent=ENST00000754841.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754841.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754841;exon_number=2;exon_id=ENSE00004103189.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12115241 12116171 . + . ID=exon:ENST00000754841.1:3;Parent=ENST00000754841.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754841.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754841;exon_number=3;exon_id=ENSE00004103203.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12097930 12143202 . + . ID=ENST00000754836.1;Parent=ENSG00000298316.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754836.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754836;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12097930 12098112 . + . ID=exon:ENST00000754836.1:1;Parent=ENST00000754836.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754836.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754836;exon_number=1;exon_id=ENSE00004103190.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12100134 12100192 . + . ID=exon:ENST00000754836.1:2;Parent=ENST00000754836.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754836.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754836;exon_number=2;exon_id=ENSE00004103189.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12103169 12103228 . + . ID=exon:ENST00000754836.1:3;Parent=ENST00000754836.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754836.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754836;exon_number=3;exon_id=ENSE00004103173.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12142943 12143202 . + . ID=exon:ENST00000754836.1:4;Parent=ENST00000754836.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754836.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754836;exon_number=4;exon_id=ENSE00004103171.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12097937 12219507 . + . ID=ENST00000754820.1;Parent=ENSG00000298316.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12097937 12098112 . + . ID=exon:ENST00000754820.1:1;Parent=ENST00000754820.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;exon_number=1;exon_id=ENSE00004103202.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12098494 12098712 . + . ID=exon:ENST00000754820.1:2;Parent=ENST00000754820.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;exon_number=2;exon_id=ENSE00004103180.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12100134 12100192 . + . ID=exon:ENST00000754820.1:3;Parent=ENST00000754820.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;exon_number=3;exon_id=ENSE00004103189.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12145999 12146121 . + . ID=exon:ENST00000754820.1:4;Parent=ENST00000754820.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;exon_number=4;exon_id=ENSE00004103196.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12205805 12205837 . + . ID=exon:ENST00000754820.1:5;Parent=ENST00000754820.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;exon_number=5;exon_id=ENSE00004103188.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12219146 12219193 . + . ID=exon:ENST00000754820.1:6;Parent=ENST00000754820.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;exon_number=6;exon_id=ENSE00004103199.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12219374 12219507 . + . ID=exon:ENST00000754820.1:7;Parent=ENST00000754820.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754820.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754820;exon_number=7;exon_id=ENSE00004103194.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12097963 12143197 . + . ID=ENST00000754840.1;Parent=ENSG00000298316.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754840.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754840;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12097963 12098112 . + . ID=exon:ENST00000754840.1:1;Parent=ENST00000754840.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754840.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754840;exon_number=1;exon_id=ENSE00004103211.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12098494 12098712 . + . ID=exon:ENST00000754840.1:2;Parent=ENST00000754840.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754840.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754840;exon_number=2;exon_id=ENSE00004103180.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12100134 12100192 . + . ID=exon:ENST00000754840.1:3;Parent=ENST00000754840.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754840.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754840;exon_number=3;exon_id=ENSE00004103189.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12126731 12126854 . + . ID=exon:ENST00000754840.1:4;Parent=ENST00000754840.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754840.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754840;exon_number=4;exon_id=ENSE00004103195.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12142943 12143197 . + . ID=exon:ENST00000754840.1:5;Parent=ENST00000754840.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754840.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754840;exon_number=5;exon_id=ENSE00004103181.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12097965 12149250 . + . ID=ENST00000754826.1;Parent=ENSG00000298316.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754826.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754826;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12097965 12098112 . + . ID=exon:ENST00000754826.1:1;Parent=ENST00000754826.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754826.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754826;exon_number=1;exon_id=ENSE00004103172.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12100134 12100192 . + . ID=exon:ENST00000754826.1:2;Parent=ENST00000754826.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754826.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754826;exon_number=2;exon_id=ENSE00004103189.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12145999 12146121 . + . ID=exon:ENST00000754826.1:3;Parent=ENST00000754826.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754826.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754826;exon_number=3;exon_id=ENSE00004103196.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12146606 12146650 . + . ID=exon:ENST00000754826.1:4;Parent=ENST00000754826.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754826.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754826;exon_number=4;exon_id=ENSE00004103197.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12147978 12149250 . + . ID=exon:ENST00000754826.1:5;Parent=ENST00000754826.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754826.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754826;exon_number=5;exon_id=ENSE00004103207.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12097972 12146760 . + . ID=ENST00000754833.1;Parent=ENSG00000298316.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754833.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754833;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12097972 12098112 . + . ID=exon:ENST00000754833.1:1;Parent=ENST00000754833.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754833.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754833;exon_number=1;exon_id=ENSE00004103192.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12098427 12098581 . + . ID=exon:ENST00000754833.1:2;Parent=ENST00000754833.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754833.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754833;exon_number=2;exon_id=ENSE00004103206.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12100134 12100192 . + . ID=exon:ENST00000754833.1:3;Parent=ENST00000754833.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754833.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754833;exon_number=3;exon_id=ENSE00004103189.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12145999 12146121 . + . ID=exon:ENST00000754833.1:4;Parent=ENST00000754833.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754833.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754833;exon_number=4;exon_id=ENSE00004103196.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12146606 12146760 . + . ID=exon:ENST00000754833.1:5;Parent=ENST00000754833.1;gene_id=ENSG00000298316.1;transcript_id=ENST00000754833.1;gene_type=lncRNA;gene_name=ENSG00000298316;transcript_type=lncRNA;transcript_name=ENST00000754833;exon_number=5;exon_id=ENSE00004103209.1;level=2;tag=basic,TAGENE +chr22 HAVANA gene 12099178 12167106 . - . ID=ENSG00000298334.1;gene_id=ENSG00000298334.1;gene_type=lncRNA;gene_name=ENSG00000298334;level=2 +chr22 HAVANA transcript 12099178 12132557 . - . ID=ENST00000754960.1;Parent=ENSG00000298334.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754960.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754960;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12132425 12132557 . - . ID=exon:ENST00000754960.1:1;Parent=ENST00000754960.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754960.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754960;exon_number=1;exon_id=ENSE00004103445.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12102147 12102239 . - . ID=exon:ENST00000754960.1:2;Parent=ENST00000754960.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754960.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754960;exon_number=2;exon_id=ENSE00004103441.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12099178 12100252 . - . ID=exon:ENST00000754960.1:3;Parent=ENST00000754960.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754960.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754960;exon_number=3;exon_id=ENSE00004103458.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12099777 12164859 . - . ID=ENST00000754958.1;Parent=ENSG00000298334.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754958.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754958;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12164723 12164859 . - . ID=exon:ENST00000754958.1:1;Parent=ENST00000754958.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754958.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754958;exon_number=1;exon_id=ENSE00004103447.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12159438 12159592 . - . ID=exon:ENST00000754958.1:2;Parent=ENST00000754958.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754958.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754958;exon_number=2;exon_id=ENSE00004103457.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12102147 12102239 . - . ID=exon:ENST00000754958.1:3;Parent=ENST00000754958.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754958.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754958;exon_number=3;exon_id=ENSE00004103441.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12099777 12100252 . - . ID=exon:ENST00000754958.1:4;Parent=ENST00000754958.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754958.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754958;exon_number=4;exon_id=ENSE00004103456.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA transcript 12099779 12164770 . - . ID=ENST00000754959.1;Parent=ENSG00000298334.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754959.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754959;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12164723 12164770 . - . ID=exon:ENST00000754959.1:1;Parent=ENST00000754959.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754959.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754959;exon_number=1;exon_id=ENSE00004103444.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12159438 12159592 . - . ID=exon:ENST00000754959.1:2;Parent=ENST00000754959.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754959.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754959;exon_number=2;exon_id=ENSE00004103457.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12111874 12112001 . - . ID=exon:ENST00000754959.1:3;Parent=ENST00000754959.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754959.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754959;exon_number=3;exon_id=ENSE00004103454.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12102147 12102239 . - . ID=exon:ENST00000754959.1:4;Parent=ENST00000754959.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754959.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754959;exon_number=4;exon_id=ENSE00004103441.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12099779 12100252 . - . ID=exon:ENST00000754959.1:5;Parent=ENST00000754959.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754959.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754959;exon_number=5;exon_id=ENSE00004103449.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12150395 12167083 . - . ID=ENST00000754964.1;Parent=ENSG00000298334.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754964.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754964;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12166830 12167083 . - . ID=exon:ENST00000754964.1:1;Parent=ENST00000754964.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754964.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754964;exon_number=1;exon_id=ENSE00004103446.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12159438 12159592 . - . ID=exon:ENST00000754964.1:2;Parent=ENST00000754964.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754964.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754964;exon_number=2;exon_id=ENSE00004103457.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12150395 12150833 . - . ID=exon:ENST00000754964.1:3;Parent=ENST00000754964.1;gene_id=ENSG00000298334.1;transcript_id=ENST00000754964.1;gene_type=lncRNA;gene_name=ENSG00000298334;transcript_type=lncRNA;transcript_name=ENST00000754964;exon_number=3;exon_id=ENSE00004103448.1;level=2;tag=basic,TAGENE +chr22 HAVANA gene 12279848 12281130 . + . ID=ENSG00000307720.1;gene_id=ENSG00000307720.1;gene_type=lncRNA;gene_name=ENSG00000307720;level=2 +chr22 HAVANA transcript 12279848 12281130 . + . ID=ENST00000828133.1;Parent=ENSG00000307720.1;gene_id=ENSG00000307720.1;transcript_id=ENST00000828133.1;gene_type=lncRNA;gene_name=ENSG00000307720;transcript_type=lncRNA;transcript_name=ENST00000828133;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12279848 12280331 . + . ID=exon:ENST00000828133.1:1;Parent=ENST00000828133.1;gene_id=ENSG00000307720.1;transcript_id=ENST00000828133.1;gene_type=lncRNA;gene_name=ENSG00000307720;transcript_type=lncRNA;transcript_name=ENST00000828133;exon_number=1;exon_id=ENSE00004240652.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12280808 12281130 . + . ID=exon:ENST00000828133.1:2;Parent=ENST00000828133.1;gene_id=ENSG00000307720.1;transcript_id=ENST00000828133.1;gene_type=lncRNA;gene_name=ENSG00000307720;transcript_type=lncRNA;transcript_name=ENST00000828133;exon_number=2;exon_id=ENSE00004240653.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA gene 12298622 12309789 . - . ID=ENSG00000300120.1;gene_id=ENSG00000300120.1;gene_type=lncRNA;gene_name=ENSG00000300120;level=2 +chr22 HAVANA transcript 12298622 12309789 . - . ID=ENST00000769194.1;Parent=ENSG00000300120.1;gene_id=ENSG00000300120.1;transcript_id=ENST00000769194.1;gene_type=lncRNA;gene_name=ENSG00000300120;transcript_type=lncRNA;transcript_name=ENST00000769194;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12309648 12309789 . - . ID=exon:ENST00000769194.1:1;Parent=ENST00000769194.1;gene_id=ENSG00000300120.1;transcript_id=ENST00000769194.1;gene_type=lncRNA;gene_name=ENSG00000300120;transcript_type=lncRNA;transcript_name=ENST00000769194;exon_number=1;exon_id=ENSE00004130103.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA exon 12298622 12298878 . - . ID=exon:ENST00000769194.1:2;Parent=ENST00000769194.1;gene_id=ENSG00000300120.1;transcript_id=ENST00000769194.1;gene_type=lncRNA;gene_name=ENSG00000300120;transcript_type=lncRNA;transcript_name=ENST00000769194;exon_number=2;exon_id=ENSE00004130102.1;level=2;tag=basic,Ensembl_canonical,GENCODE_Primary,TAGENE +chr22 HAVANA gene 12602041 12629211 . + . ID=ENSG00000310236.1;gene_id=ENSG00000310236.1;gene_type=lncRNA;gene_name=ENSG00000310236;level=2;tag=overlapping_locus,overlaps_pseudogene +chr22 HAVANA transcript 12602302 12626718 . + . ID=ENST00000848488.1;Parent=ENSG00000310236.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848488.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848488;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12602302 12602527 . + . ID=exon:ENST00000848488.1:1;Parent=ENST00000848488.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848488.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848488;exon_number=1;exon_id=ENSE00004278034.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12603297 12603533 . + . ID=exon:ENST00000848488.1:2;Parent=ENST00000848488.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848488.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848488;exon_number=2;exon_id=ENSE00004278015.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12604670 12604739 . + . ID=exon:ENST00000848488.1:3;Parent=ENST00000848488.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848488.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848488;exon_number=3;exon_id=ENSE00004278024.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12624242 12624333 . + . ID=exon:ENST00000848488.1:4;Parent=ENST00000848488.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848488.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848488;exon_number=4;exon_id=ENSE00004278032.1;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12625317 12626718 . + . ID=exon:ENST00000848488.1:5;Parent=ENST00000848488.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848488.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848488;exon_number=5;exon_id=ENSE00004278036.1;level=2;tag=basic,TAGENE +chr22 HAVANA transcript 12602329 12629201 . + . ID=ENST00000848485.1;Parent=ENSG00000310236.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848485.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848485;level=2;tag=basic,TAGENE +chr22 HAVANA exon 12602329 12602527 . + . ID=exon:ENST00000848485.1:1;Parent=ENST00000848485.1;gene_id=ENSG00000310236.1;transcript_id=ENST00000848485.1;gene_type=lncRNA;gene_name=ENSG00000310236;transcript_type=lncRNA;transcript_name=ENST00000848485;exon_number=1;exon_id=ENSE00004278028.1;level=2;tag=basic,TAGENE diff --git a/test/fixtures/real/gencode/gencode.v50.basic.chr22.gtf b/test/fixtures/real/gencode/gencode.v50.basic.chr22.gtf new file mode 100644 index 0000000..442d284 --- /dev/null +++ b/test/fixtures/real/gencode/gencode.v50.basic.chr22.gtf @@ -0,0 +1,305 @@ +##description: evidence-based annotation of the human genome (GRCh38), version 50 (Ensembl 116) +##provider: GENCODE +##contact: gencode-help@ebi.ac.uk +##format: gtf +##date: 2026-04-08 +chr22 HAVANA gene 10524345 10529164 . - . gene_id "ENSG00000294541.1"; gene_type "lncRNA"; gene_name "ENSG00000294541"; level 2; +chr22 HAVANA transcript 10524345 10529164 . - . gene_id "ENSG00000294541.1"; transcript_id "ENST00000724296.1"; gene_type "lncRNA"; gene_name "ENSG00000294541"; transcript_type "lncRNA"; transcript_name "ENST00000724296"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 10529036 10529164 . - . gene_id "ENSG00000294541.1"; transcript_id "ENST00000724296.1"; gene_type "lncRNA"; gene_name "ENSG00000294541"; transcript_type "lncRNA"; transcript_name "ENST00000724296"; exon_number 1; exon_id "ENSE00004046862.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 10527853 10528040 . - . gene_id "ENSG00000294541.1"; transcript_id "ENST00000724296.1"; gene_type "lncRNA"; gene_name "ENSG00000294541"; transcript_type "lncRNA"; transcript_name "ENST00000724296"; exon_number 2; exon_id "ENSE00004046860.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 10524345 10524446 . - . gene_id "ENSG00000294541.1"; transcript_id "ENST00000724296.1"; gene_type "lncRNA"; gene_name "ENSG00000294541"; transcript_type "lncRNA"; transcript_name "ENST00000724296"; exon_number 3; exon_id "ENSE00004046861.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 ENSEMBL gene 10736171 10736283 . - . gene_id "ENSG00000277248.1"; gene_type "snRNA"; gene_name "U2"; level 3; +chr22 ENSEMBL transcript 10736171 10736283 . - . gene_id "ENSG00000277248.1"; transcript_id "ENST00000615943.1"; gene_type "snRNA"; gene_name "U2"; transcript_type "snRNA"; transcript_name "U2.14-201"; level 3; transcript_support_level "NA"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; +chr22 ENSEMBL exon 10736171 10736283 . - . gene_id "ENSG00000277248.1"; transcript_id "ENST00000615943.1"; gene_type "snRNA"; gene_name "U2"; transcript_type "snRNA"; transcript_name "U2.14-201"; exon_number 1; exon_id "ENSE00003736336.1"; level 3; transcript_support_level "NA"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; +chr22 HAVANA gene 10742050 10753085 . + . gene_id "ENSG00000301473.1"; gene_type "lncRNA"; gene_name "ENSG00000301473"; level 2; +chr22 HAVANA transcript 10742092 10753081 . + . gene_id "ENSG00000301473.1"; transcript_id "ENST00000779065.1"; gene_type "lncRNA"; gene_name "ENSG00000301473"; transcript_type "lncRNA"; transcript_name "ENST00000779065"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10742092 10742191 . + . gene_id "ENSG00000301473.1"; transcript_id "ENST00000779065.1"; gene_type "lncRNA"; gene_name "ENSG00000301473"; transcript_type "lncRNA"; transcript_name "ENST00000779065"; exon_number 1; exon_id "ENSE00004149143.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10749498 10749658 . + . gene_id "ENSG00000301473.1"; transcript_id "ENST00000779065.1"; gene_type "lncRNA"; gene_name "ENSG00000301473"; transcript_type "lncRNA"; transcript_name "ENST00000779065"; exon_number 2; exon_id "ENSE00004149144.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10752760 10753081 . + . gene_id "ENSG00000301473.1"; transcript_id "ENST00000779065.1"; gene_type "lncRNA"; gene_name "ENSG00000301473"; transcript_type "lncRNA"; transcript_name "ENST00000779065"; exon_number 3; exon_id "ENSE00004149147.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA gene 10752636 10754413 . - . gene_id "ENSG00000301496.1"; gene_type "lncRNA"; gene_name "ENSG00000301496"; level 2; +chr22 HAVANA transcript 10752636 10754413 . - . gene_id "ENSG00000301496.1"; transcript_id "ENST00000779294.1"; gene_type "lncRNA"; gene_name "ENSG00000301496"; transcript_type "lncRNA"; transcript_name "ENST00000779294"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 10754322 10754413 . - . gene_id "ENSG00000301496.1"; transcript_id "ENST00000779294.1"; gene_type "lncRNA"; gene_name "ENSG00000301496"; transcript_type "lncRNA"; transcript_name "ENST00000779294"; exon_number 1; exon_id "ENSE00004149605.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 10752636 10752913 . - . gene_id "ENSG00000301496.1"; transcript_id "ENST00000779294.1"; gene_type "lncRNA"; gene_name "ENSG00000301496"; transcript_type "lncRNA"; transcript_name "ENST00000779294"; exon_number 2; exon_id "ENSE00004149606.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA gene 10939388 10961338 . - . gene_id "ENSG00000283047.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; level 2; hgnc_id "HGNC:51765"; tag "overlapping_locus"; havana_gene "OTTHUMG00000191577.1"; +chr22 HAVANA transcript 10939388 10961338 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10961283 10961338 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 1; exon_id "ENSE00003786612.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10959067 10959136 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 2; exon_id "ENSE00003789146.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10950049 10950174 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 3; exon_id "ENSE00003786193.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10949212 10949269 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 4; exon_id "ENSE00003784997.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10947304 10947418 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 5; exon_id "ENSE00003787541.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10944967 10945053 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 6; exon_id "ENSE00003785466.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10941691 10941780 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 7; exon_id "ENSE00003787209.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10940597 10940707 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 8; exon_id "ENSE00003791492.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA exon 10939388 10939423 . - . gene_id "ENSG00000283047.1"; transcript_id "ENST00000635667.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "FRG1FP"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "FRG1FP-201"; exon_number 9; exon_id "ENSE00003790077.1"; level 2; transcript_support_level "NA"; hgnc_id "HGNC:51765"; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000191577.1"; havana_transcript "OTTHUMT00000488611.1"; +chr22 HAVANA gene 10941695 10961693 . - . gene_id "ENSG00000303605.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; level 2; tag "overlapping_locus"; tag "overlaps_pseudogene"; +chr22 HAVANA transcript 10941695 10961556 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10960994 10961556 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 1; exon_id "ENSE00004181266.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10960278 10960431 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 2; exon_id "ENSE00004181253.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10959067 10959136 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 3; exon_id "ENSE00004181258.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10950049 10950174 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 4; exon_id "ENSE00004181255.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10949212 10949269 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 5; exon_id "ENSE00004181254.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10947304 10947418 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 6; exon_id "ENSE00004181267.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10944967 10945053 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 7; exon_id "ENSE00004181264.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10941695 10941780 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796039.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796039"; exon_number 8; exon_id "ENSE00004181259.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 10944590 10961586 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10961283 10961586 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; exon_number 1; exon_id "ENSE00004181257.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10960332 10960514 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; exon_number 2; exon_id "ENSE00004181260.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10959067 10959136 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; exon_number 3; exon_id "ENSE00004181258.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10950049 10950174 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; exon_number 4; exon_id "ENSE00004181255.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10949212 10949269 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; exon_number 5; exon_id "ENSE00004181254.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10947304 10947418 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; exon_number 6; exon_id "ENSE00004181267.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 10944590 10945053 . - . gene_id "ENSG00000303605.1"; transcript_id "ENST00000796042.1"; gene_type "lncRNA"; gene_name "ENSG00000303605"; transcript_type "lncRNA"; transcript_name "ENST00000796042"; exon_number 7; exon_id "ENSE00004181265.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA gene 11066268 11068174 . + . gene_id "ENSG00000279973.3"; gene_type "lncRNA"; gene_name "ENSG00000279973"; level 2; havana_gene "OTTHUMG00000192006.1"; +chr22 HAVANA transcript 11066268 11068174 . + . gene_id "ENSG00000279973.3"; transcript_id "ENST00000624155.3"; gene_type "lncRNA"; gene_name "ENSG00000279973"; transcript_type "lncRNA"; transcript_name "ENST00000624155"; level 2; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; havana_gene "OTTHUMG00000192006.1"; havana_transcript "OTTHUMT00000491988.1"; +chr22 HAVANA exon 11066268 11066515 . + . gene_id "ENSG00000279973.3"; transcript_id "ENST00000624155.3"; gene_type "lncRNA"; gene_name "ENSG00000279973"; transcript_type "lncRNA"; transcript_name "ENST00000624155"; exon_number 1; exon_id "ENSE00004077563.1"; level 2; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; havana_gene "OTTHUMG00000192006.1"; havana_transcript "OTTHUMT00000491988.1"; +chr22 HAVANA exon 11067985 11068174 . + . gene_id "ENSG00000279973.3"; transcript_id "ENST00000624155.3"; gene_type "lncRNA"; gene_name "ENSG00000279973"; transcript_type "lncRNA"; transcript_name "ENST00000624155"; exon_number 2; exon_id "ENSE00003758861.2"; level 2; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; havana_gene "OTTHUMG00000192006.1"; havana_transcript "OTTHUMT00000491988.1"; +chr22 HAVANA gene 11124337 11125705 . + . gene_id "ENSG00000226444.2"; gene_type "processed_pseudogene"; gene_name "ACTR3BP7"; level 1; hgnc_id "HGNC:54971"; tag "pseudo_consens"; havana_gene "OTTHUMG00000140398.2"; +chr22 HAVANA transcript 11124337 11125705 . + . gene_id "ENSG00000226444.2"; transcript_id "ENST00000422332.1"; gene_type "processed_pseudogene"; gene_name "ACTR3BP7"; transcript_type "processed_pseudogene"; transcript_name "ACTR3BP7-201"; level 1; transcript_support_level "NA"; hgnc_id "HGNC:54971"; ont "PGO:0000004"; tag "pseudo_consens"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000140398.2"; havana_transcript "OTTHUMT00000277200.2"; +chr22 HAVANA exon 11124337 11124379 . + . gene_id "ENSG00000226444.2"; transcript_id "ENST00000422332.1"; gene_type "processed_pseudogene"; gene_name "ACTR3BP7"; transcript_type "processed_pseudogene"; transcript_name "ACTR3BP7-201"; exon_number 1; exon_id "ENSE00001616995.1"; level 1; transcript_support_level "NA"; hgnc_id "HGNC:54971"; ont "PGO:0000004"; tag "pseudo_consens"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000140398.2"; havana_transcript "OTTHUMT00000277200.2"; +chr22 HAVANA exon 11124508 11125705 . + . gene_id "ENSG00000226444.2"; transcript_id "ENST00000422332.1"; gene_type "processed_pseudogene"; gene_name "ACTR3BP7"; transcript_type "processed_pseudogene"; transcript_name "ACTR3BP7-201"; exon_number 2; exon_id "ENSE00001776473.1"; level 1; transcript_support_level "NA"; hgnc_id "HGNC:54971"; ont "PGO:0000004"; tag "pseudo_consens"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000140398.2"; havana_transcript "OTTHUMT00000277200.2"; +chr22 HAVANA gene 11146119 11147823 . + . gene_id "ENSG00000294022.1"; gene_type "lncRNA"; gene_name "ENSG00000294022"; level 2; +chr22 HAVANA transcript 11146119 11147823 . + . gene_id "ENSG00000294022.1"; transcript_id "ENST00000720620.1"; gene_type "lncRNA"; gene_name "ENSG00000294022"; transcript_type "lncRNA"; transcript_name "ENST00000720620"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 11146119 11146180 . + . gene_id "ENSG00000294022.1"; transcript_id "ENST00000720620.1"; gene_type "lncRNA"; gene_name "ENSG00000294022"; transcript_type "lncRNA"; transcript_name "ENST00000720620"; exon_number 1; exon_id "ENSE00004039547.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 11146349 11146429 . + . gene_id "ENSG00000294022.1"; transcript_id "ENST00000720620.1"; gene_type "lncRNA"; gene_name "ENSG00000294022"; transcript_type "lncRNA"; transcript_name "ENST00000720620"; exon_number 2; exon_id "ENSE00004039545.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 11147580 11147823 . + . gene_id "ENSG00000294022.1"; transcript_id "ENST00000720620.1"; gene_type "lncRNA"; gene_name "ENSG00000294022"; transcript_type "lncRNA"; transcript_name "ENST00000720620"; exon_number 3; exon_id "ENSE00004039546.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 ENSEMBL gene 11249809 11249959 . - . gene_id "ENSG00000276871.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; level 3; +chr22 ENSEMBL transcript 11249809 11249959 . - . gene_id "ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; level 3; transcript_support_level "NA"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; +chr22 ENSEMBL exon 11249809 11249959 . - . gene_id "ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; exon_number 1; exon_id "ENSE00003735240.1"; level 3; transcript_support_level "NA"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; +chr22 HAVANA gene 11474744 11479643 . + . gene_id "ENSG00000288262.1"; gene_type "unprocessed_pseudogene"; gene_name "ZNF73P"; level 2; hgnc_id "HGNC:13143"; havana_gene "OTTHUMG00000195920.1"; +chr22 HAVANA transcript 11474744 11479643 . + . gene_id "ENSG00000288262.1"; transcript_id "ENST00000672261.1"; gene_type "unprocessed_pseudogene"; gene_name "ZNF73P"; transcript_type "unprocessed_pseudogene"; transcript_name "ZNF73P-201"; level 2; hgnc_id "HGNC:13143"; ont "PGO:0000005"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000195920.1"; havana_transcript "OTTHUMT00000529609.1"; +chr22 HAVANA exon 11474744 11474904 . + . gene_id "ENSG00000288262.1"; transcript_id "ENST00000672261.1"; gene_type "unprocessed_pseudogene"; gene_name "ZNF73P"; transcript_type "unprocessed_pseudogene"; transcript_name "ZNF73P-201"; exon_number 1; exon_id "ENSE00003893399.1"; level 2; hgnc_id "HGNC:13143"; ont "PGO:0000005"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000195920.1"; havana_transcript "OTTHUMT00000529609.1"; +chr22 HAVANA exon 11475146 11475238 . + . gene_id "ENSG00000288262.1"; transcript_id "ENST00000672261.1"; gene_type "unprocessed_pseudogene"; gene_name "ZNF73P"; transcript_type "unprocessed_pseudogene"; transcript_name "ZNF73P-201"; exon_number 2; exon_id "ENSE00003891926.1"; level 2; hgnc_id "HGNC:13143"; ont "PGO:0000005"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000195920.1"; havana_transcript "OTTHUMT00000529609.1"; +chr22 HAVANA exon 11477178 11479643 . + . gene_id "ENSG00000288262.1"; transcript_id "ENST00000672261.1"; gene_type "unprocessed_pseudogene"; gene_name "ZNF73P"; transcript_type "unprocessed_pseudogene"; transcript_name "ZNF73P-201"; exon_number 3; exon_id "ENSE00003892093.1"; level 2; hgnc_id "HGNC:13143"; ont "PGO:0000005"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000195920.1"; havana_transcript "OTTHUMT00000529609.1"; +chr22 HAVANA gene 11707145 11955470 . + . gene_id "ENSG00000290397.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; level 2; tag "overlaps_pseudogene"; +chr22 HAVANA transcript 11707176 11886438 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11707176 11707423 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 1; exon_id "ENSE00004279894.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11832761 11832915 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 2; exon_id "ENSE00003884543.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11867115 11867145 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 3; exon_id "ENSE00003864175.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11869829 11869898 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 4; exon_id "ENSE00003886323.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11870756 11870787 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 5; exon_id "ENSE00004279888.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11873841 11873925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 6; exon_id "ENSE00003876297.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876104 11876132 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 7; exon_id "ENSE00003884551.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876224 11876296 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 8; exon_id "ENSE00003880389.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11882268 11882338 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 9; exon_id "ENSE00003877785.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11886401 11886438 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849404.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849404"; exon_number 10; exon_id "ENSE00004279874.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11707179 11869574 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849410.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849410"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11707179 11707423 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849410.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849410"; exon_number 1; exon_id "ENSE00004279876.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11832761 11832915 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849410.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849410"; exon_number 2; exon_id "ENSE00003884543.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11867115 11869574 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849410.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849410"; exon_number 3; exon_id "ENSE00004279870.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11709407 11715712 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849442.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849442"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11709407 11709542 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849442.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849442"; exon_number 1; exon_id "ENSE00004279908.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11714674 11715712 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849442.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849442"; exon_number 2; exon_id "ENSE00004279903.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11825264 11833819 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849438.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849438"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11825264 11825547 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849438.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849438"; exon_number 1; exon_id "ENSE00004279895.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11832761 11833819 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849438.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849438"; exon_number 2; exon_id "ENSE00004279887.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11827522 11889435 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11827522 11827658 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 1; exon_id "ENSE00004279914.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11832761 11832915 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 2; exon_id "ENSE00003884543.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11873844 11873925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 3; exon_id "ENSE00004279875.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876104 11876132 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 4; exon_id "ENSE00003884551.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876224 11876296 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 5; exon_id "ENSE00003880389.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11882268 11882338 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 6; exon_id "ENSE00003877785.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11886401 11886565 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 7; exon_id "ENSE00004811648.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11887952 11888146 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 8; exon_id "ENSE00004279873.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11889310 11889435 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849415.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849415"; exon_number 9; exon_id "ENSE00004279905.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11827522 11910358 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11827522 11827658 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 1; exon_id "ENSE00004279914.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11832761 11832915 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 2; exon_id "ENSE00003884543.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11867115 11867145 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 3; exon_id "ENSE00003864175.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11869829 11869898 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 4; exon_id "ENSE00003886323.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11872163 11872354 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 5; exon_id "ENSE00003874242.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11873841 11873925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 6; exon_id "ENSE00003876297.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11876104 11876132 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 7; exon_id "ENSE00003884551.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11876224 11876296 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 8; exon_id "ENSE00003880389.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11882268 11882338 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 9; exon_id "ENSE00003877785.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11886401 11886565 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 10; exon_id "ENSE00004811648.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11887952 11888146 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 11; exon_id "ENSE00004279873.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11889310 11890230 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 12; exon_id "ENSE00004811640.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11891782 11891931 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 13; exon_id "ENSE00004811641.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11902861 11903142 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 14; exon_id "ENSE00004811643.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11903787 11904000 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 15; exon_id "ENSE00004811645.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11905337 11905557 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 16; exon_id "ENSE00003885180.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA exon 11910166 11910358 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000657566.2"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000657566"; exon_number 17; exon_id "ENSE00003868543.1"; level 2; tag "RNA_Seq_supported_only"; tag "basic"; tag "TAGENE"; havana_transcript "OTTHUMT00000504859.1"; +chr22 HAVANA transcript 11827523 11870977 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849423.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849423"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11827523 11827658 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849423.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849423"; exon_number 1; exon_id "ENSE00004279921.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11832761 11832915 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849423.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849423"; exon_number 2; exon_id "ENSE00003884543.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11867115 11867145 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849423.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849423"; exon_number 3; exon_id "ENSE00003864175.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11869054 11869125 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849423.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849423"; exon_number 4; exon_id "ENSE00004279896.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11869829 11870977 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849423.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849423"; exon_number 5; exon_id "ENSE00004279907.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11859802 11889426 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11859802 11859927 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 1; exon_id "ENSE00004279872.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11867115 11867145 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 2; exon_id "ENSE00003864175.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11869829 11869898 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 3; exon_id "ENSE00003886323.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11872163 11872358 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 4; exon_id "ENSE00004279884.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11873841 11873925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 5; exon_id "ENSE00003876297.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876104 11876132 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 6; exon_id "ENSE00003884551.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876224 11876296 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 7; exon_id "ENSE00003880389.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11882268 11882338 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 8; exon_id "ENSE00003877785.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11886401 11886565 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 9; exon_id "ENSE00004811648.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11887952 11888146 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 10; exon_id "ENSE00004279873.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11889310 11889426 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849431.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849431"; exon_number 11; exon_id "ENSE00004279891.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11859817 11890645 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11859817 11859927 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 1; exon_id "ENSE00004279878.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11867115 11867145 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 2; exon_id "ENSE00003864175.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11869054 11869125 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 3; exon_id "ENSE00004279896.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11869829 11869898 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 4; exon_id "ENSE00003886323.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11872163 11872354 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 5; exon_id "ENSE00003874242.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11873844 11873925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 6; exon_id "ENSE00004279875.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876104 11876132 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 7; exon_id "ENSE00003884551.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876224 11876296 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 8; exon_id "ENSE00003880389.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11881986 11882119 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 9; exon_id "ENSE00004279918.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11882268 11882338 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 10; exon_id "ENSE00003877785.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11886401 11886565 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 11; exon_id "ENSE00004811648.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11887952 11888146 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 12; exon_id "ENSE00004279873.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11889310 11890645 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849426.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849426"; exon_number 13; exon_id "ENSE00004279932.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11859827 11889925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11859827 11859927 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 1; exon_id "ENSE00004279925.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11867115 11867145 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 2; exon_id "ENSE00003864175.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11869829 11869898 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 3; exon_id "ENSE00003886323.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11873841 11873925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 4; exon_id "ENSE00003876297.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876104 11876132 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 5; exon_id "ENSE00003884551.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11876224 11876296 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 6; exon_id "ENSE00003880389.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11882268 11882338 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 7; exon_id "ENSE00003877785.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11886401 11886565 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 8; exon_id "ENSE00004811648.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11887952 11888146 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 9; exon_id "ENSE00004279873.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11889310 11889925 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849428.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849428"; exon_number 10; exon_id "ENSE00004279917.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11897376 11915770 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849433.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849433"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11897376 11897467 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849433.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849433"; exon_number 1; exon_id "ENSE00004279885.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11910166 11910219 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849433.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849433"; exon_number 2; exon_id "ENSE00004279897.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11913040 11913192 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849433.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849433"; exon_number 3; exon_id "ENSE00004279916.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11914501 11915770 . + . gene_id "ENSG00000290397.2"; transcript_id "ENST00000849433.1"; gene_type "lncRNA"; gene_name "ENSG00000290397"; transcript_type "lncRNA"; transcript_name "ENST00000849433"; exon_number 4; exon_id "ENSE00004279913.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA gene 11832287 11974294 . - . gene_id "ENSG00000310416.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; level 2; +chr22 HAVANA transcript 11832621 11974223 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849584.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849584"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11974138 11974223 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849584.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849584"; exon_number 1; exon_id "ENSE00004280383.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11973415 11973633 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849584.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849584"; exon_number 2; exon_id "ENSE00004280322.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849584.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849584"; exon_number 3; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11868679 11868961 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849584.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849584"; exon_number 4; exon_id "ENSE00004280275.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11846227 11846349 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849584.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849584"; exon_number 5; exon_id "ENSE00004280308.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11832621 11832954 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849584.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849584"; exon_number 6; exon_id "ENSE00004280351.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11833182 11974184 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849596.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849596"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11974015 11974184 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849596.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849596"; exon_number 1; exon_id "ENSE00004280387.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11973277 11973364 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849596.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849596"; exon_number 2; exon_id "ENSE00004280295.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849596.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849596"; exon_number 3; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11846227 11846349 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849596.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849596"; exon_number 4; exon_id "ENSE00004280308.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11833182 11833801 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849596.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849596"; exon_number 5; exon_id "ENSE00004280310.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11843099 11974198 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11974015 11974198 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; exon_number 1; exon_id "ENSE00004280342.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; exon_number 2; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11878920 11879007 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; exon_number 3; exon_id "ENSE00004280373.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11868679 11868961 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; exon_number 4; exon_id "ENSE00004280275.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11846227 11846349 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; exon_number 5; exon_id "ENSE00004280308.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11845698 11845742 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; exon_number 6; exon_id "ENSE00004280312.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11843099 11844371 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849602.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849602"; exon_number 7; exon_id "ENSE00004280278.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11849156 11974214 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849617.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849617"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11974138 11974214 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849617.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849617"; exon_number 1; exon_id "ENSE00004280375.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849617.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849617"; exon_number 2; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11967956 11968015 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849617.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849617"; exon_number 3; exon_id "ENSE00004280354.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11868679 11868946 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849617.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849617"; exon_number 4; exon_id "ENSE00004280360.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11849156 11849410 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849617.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849617"; exon_number 5; exon_id "ENSE00004280371.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11909005 11974189 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849633.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849633"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11973415 11974189 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849633.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849633"; exon_number 1; exon_id "ENSE00004280293.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849633.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849633"; exon_number 2; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11910629 11910824 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849633.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849633"; exon_number 3; exon_id "ENSE00004280299.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11909005 11910230 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849633.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849633"; exon_number 4; exon_id "ENSE00004280355.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11910581 11974223 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849636.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849636"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11973931 11974223 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849636.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849636"; exon_number 1; exon_id "ENSE00004280305.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849636.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849636"; exon_number 2; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11925034 11925073 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849636.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849636"; exon_number 3; exon_id "ENSE00004280384.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11912216 11912317 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849636.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849636"; exon_number 4; exon_id "ENSE00004280377.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11910581 11911026 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849636.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849636"; exon_number 5; exon_id "ENSE00004280376.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11925292 11974155 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849642.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849642"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11973931 11974155 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849642.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849642"; exon_number 1; exon_id "ENSE00004280349.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849642.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849642"; exon_number 2; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11928542 11929140 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849642.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849642"; exon_number 3; exon_id "ENSE00004280343.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11925292 11926287 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849642.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849642"; exon_number 4; exon_id "ENSE00004280277.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 11928502 11974185 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849650.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849650"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11974015 11974185 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849650.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849650"; exon_number 1; exon_id "ENSE00004280331.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11973415 11973607 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849650.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849650"; exon_number 2; exon_id "ENSE00004280276.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11971940 11971998 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849650.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849650"; exon_number 3; exon_id "ENSE00004280282.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 11928502 11929140 . - . gene_id "ENSG00000310416.1"; transcript_id "ENST00000849650.1"; gene_type "lncRNA"; gene_name "ENSG00000310416"; transcript_type "lncRNA"; transcript_name "ENST00000849650"; exon_number 4; exon_id "ENSE00004280352.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA gene 11883602 11904000 . + . gene_id "ENSG00000286406.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; level 2; havana_gene "OTTHUMG00000193804.1"; +chr22 HAVANA transcript 11883602 11904000 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA exon 11883602 11884628 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; exon_number 1; exon_id "ENSE00003871741.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA exon 11886401 11886565 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; exon_number 2; exon_id "ENSE00003869821.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA exon 11887952 11888146 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; exon_number 3; exon_id "ENSE00003858885.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA exon 11889310 11890230 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; exon_number 4; exon_id "ENSE00003859113.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA exon 11891782 11891931 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; exon_number 5; exon_id "ENSE00003859245.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA exon 11902861 11903142 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; exon_number 6; exon_id "ENSE00003861322.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA exon 11903787 11904000 . + . gene_id "ENSG00000286406.2"; transcript_id "ENST00000657645.1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "ENSG00000286406"; transcript_type "transcribed_unprocessed_pseudogene"; transcript_name "ENST00000657645"; exon_number 7; exon_id "ENSE00003862233.1"; level 2; ont "PGO:0000005"; ont "PGO:0000019"; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; havana_gene "OTTHUMG00000193804.1"; havana_transcript "OTTHUMT00000504860.1"; +chr22 HAVANA gene 12038112 12056544 . - . gene_id "ENSG00000296155.1"; gene_type "lncRNA"; gene_name "ENSG00000296155"; level 2; +chr22 HAVANA transcript 12038112 12056544 . - . gene_id "ENSG00000296155.1"; transcript_id "ENST00000736916.1"; gene_type "lncRNA"; gene_name "ENSG00000296155"; transcript_type "lncRNA"; transcript_name "ENST00000736916"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12056492 12056544 . - . gene_id "ENSG00000296155.1"; transcript_id "ENST00000736916.1"; gene_type "lncRNA"; gene_name "ENSG00000296155"; transcript_type "lncRNA"; transcript_name "ENST00000736916"; exon_number 1; exon_id "ENSE00004070662.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12038112 12038831 . - . gene_id "ENSG00000296155.1"; transcript_id "ENST00000736916.1"; gene_type "lncRNA"; gene_name "ENSG00000296155"; transcript_type "lncRNA"; transcript_name "ENST00000736916"; exon_number 2; exon_id "ENSE00004070665.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA gene 12097900 12219507 . + . gene_id "ENSG00000298316.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; level 2; +chr22 HAVANA transcript 12097902 12116171 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754841.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754841"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12097902 12098112 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754841.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754841"; exon_number 1; exon_id "ENSE00004103176.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12100134 12100192 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754841.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754841"; exon_number 2; exon_id "ENSE00004103189.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12115241 12116171 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754841.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754841"; exon_number 3; exon_id "ENSE00004103203.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12097930 12143202 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754836.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754836"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12097930 12098112 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754836.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754836"; exon_number 1; exon_id "ENSE00004103190.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12100134 12100192 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754836.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754836"; exon_number 2; exon_id "ENSE00004103189.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12103169 12103228 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754836.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754836"; exon_number 3; exon_id "ENSE00004103173.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12142943 12143202 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754836.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754836"; exon_number 4; exon_id "ENSE00004103171.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12097937 12219507 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12097937 12098112 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; exon_number 1; exon_id "ENSE00004103202.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12098494 12098712 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; exon_number 2; exon_id "ENSE00004103180.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12100134 12100192 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; exon_number 3; exon_id "ENSE00004103189.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12145999 12146121 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; exon_number 4; exon_id "ENSE00004103196.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12205805 12205837 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; exon_number 5; exon_id "ENSE00004103188.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12219146 12219193 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; exon_number 6; exon_id "ENSE00004103199.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12219374 12219507 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754820.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754820"; exon_number 7; exon_id "ENSE00004103194.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12097963 12143197 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754840.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754840"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12097963 12098112 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754840.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754840"; exon_number 1; exon_id "ENSE00004103211.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12098494 12098712 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754840.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754840"; exon_number 2; exon_id "ENSE00004103180.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12100134 12100192 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754840.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754840"; exon_number 3; exon_id "ENSE00004103189.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12126731 12126854 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754840.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754840"; exon_number 4; exon_id "ENSE00004103195.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12142943 12143197 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754840.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754840"; exon_number 5; exon_id "ENSE00004103181.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12097965 12149250 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754826.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754826"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12097965 12098112 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754826.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754826"; exon_number 1; exon_id "ENSE00004103172.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12100134 12100192 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754826.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754826"; exon_number 2; exon_id "ENSE00004103189.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12145999 12146121 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754826.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754826"; exon_number 3; exon_id "ENSE00004103196.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12146606 12146650 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754826.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754826"; exon_number 4; exon_id "ENSE00004103197.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12147978 12149250 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754826.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754826"; exon_number 5; exon_id "ENSE00004103207.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12097972 12146760 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754833.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754833"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12097972 12098112 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754833.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754833"; exon_number 1; exon_id "ENSE00004103192.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12098427 12098581 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754833.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754833"; exon_number 2; exon_id "ENSE00004103206.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12100134 12100192 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754833.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754833"; exon_number 3; exon_id "ENSE00004103189.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12145999 12146121 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754833.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754833"; exon_number 4; exon_id "ENSE00004103196.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12146606 12146760 . + . gene_id "ENSG00000298316.1"; transcript_id "ENST00000754833.1"; gene_type "lncRNA"; gene_name "ENSG00000298316"; transcript_type "lncRNA"; transcript_name "ENST00000754833"; exon_number 5; exon_id "ENSE00004103209.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA gene 12099178 12167106 . - . gene_id "ENSG00000298334.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; level 2; +chr22 HAVANA transcript 12099178 12132557 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754960.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754960"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12132425 12132557 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754960.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754960"; exon_number 1; exon_id "ENSE00004103445.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12102147 12102239 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754960.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754960"; exon_number 2; exon_id "ENSE00004103441.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12099178 12100252 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754960.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754960"; exon_number 3; exon_id "ENSE00004103458.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12099777 12164859 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754958.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754958"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12164723 12164859 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754958.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754958"; exon_number 1; exon_id "ENSE00004103447.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12159438 12159592 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754958.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754958"; exon_number 2; exon_id "ENSE00004103457.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12102147 12102239 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754958.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754958"; exon_number 3; exon_id "ENSE00004103441.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12099777 12100252 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754958.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754958"; exon_number 4; exon_id "ENSE00004103456.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA transcript 12099779 12164770 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754959.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754959"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12164723 12164770 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754959.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754959"; exon_number 1; exon_id "ENSE00004103444.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12159438 12159592 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754959.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754959"; exon_number 2; exon_id "ENSE00004103457.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12111874 12112001 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754959.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754959"; exon_number 3; exon_id "ENSE00004103454.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12102147 12102239 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754959.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754959"; exon_number 4; exon_id "ENSE00004103441.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12099779 12100252 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754959.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754959"; exon_number 5; exon_id "ENSE00004103449.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12150395 12167083 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754964.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754964"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12166830 12167083 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754964.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754964"; exon_number 1; exon_id "ENSE00004103446.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12159438 12159592 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754964.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754964"; exon_number 2; exon_id "ENSE00004103457.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12150395 12150833 . - . gene_id "ENSG00000298334.1"; transcript_id "ENST00000754964.1"; gene_type "lncRNA"; gene_name "ENSG00000298334"; transcript_type "lncRNA"; transcript_name "ENST00000754964"; exon_number 3; exon_id "ENSE00004103448.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA gene 12279848 12281130 . + . gene_id "ENSG00000307720.1"; gene_type "lncRNA"; gene_name "ENSG00000307720"; level 2; +chr22 HAVANA transcript 12279848 12281130 . + . gene_id "ENSG00000307720.1"; transcript_id "ENST00000828133.1"; gene_type "lncRNA"; gene_name "ENSG00000307720"; transcript_type "lncRNA"; transcript_name "ENST00000828133"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12279848 12280331 . + . gene_id "ENSG00000307720.1"; transcript_id "ENST00000828133.1"; gene_type "lncRNA"; gene_name "ENSG00000307720"; transcript_type "lncRNA"; transcript_name "ENST00000828133"; exon_number 1; exon_id "ENSE00004240652.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12280808 12281130 . + . gene_id "ENSG00000307720.1"; transcript_id "ENST00000828133.1"; gene_type "lncRNA"; gene_name "ENSG00000307720"; transcript_type "lncRNA"; transcript_name "ENST00000828133"; exon_number 2; exon_id "ENSE00004240653.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA gene 12298622 12309789 . - . gene_id "ENSG00000300120.1"; gene_type "lncRNA"; gene_name "ENSG00000300120"; level 2; +chr22 HAVANA transcript 12298622 12309789 . - . gene_id "ENSG00000300120.1"; transcript_id "ENST00000769194.1"; gene_type "lncRNA"; gene_name "ENSG00000300120"; transcript_type "lncRNA"; transcript_name "ENST00000769194"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12309648 12309789 . - . gene_id "ENSG00000300120.1"; transcript_id "ENST00000769194.1"; gene_type "lncRNA"; gene_name "ENSG00000300120"; transcript_type "lncRNA"; transcript_name "ENST00000769194"; exon_number 1; exon_id "ENSE00004130103.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA exon 12298622 12298878 . - . gene_id "ENSG00000300120.1"; transcript_id "ENST00000769194.1"; gene_type "lncRNA"; gene_name "ENSG00000300120"; transcript_type "lncRNA"; transcript_name "ENST00000769194"; exon_number 2; exon_id "ENSE00004130102.1"; level 2; tag "basic"; tag "Ensembl_canonical"; tag "GENCODE_Primary"; tag "TAGENE"; +chr22 HAVANA gene 12602041 12629211 . + . gene_id "ENSG00000310236.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; level 2; tag "overlapping_locus"; tag "overlaps_pseudogene"; +chr22 HAVANA transcript 12602302 12626718 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848488.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848488"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12602302 12602527 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848488.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848488"; exon_number 1; exon_id "ENSE00004278034.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12603297 12603533 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848488.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848488"; exon_number 2; exon_id "ENSE00004278015.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12604670 12604739 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848488.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848488"; exon_number 3; exon_id "ENSE00004278024.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12624242 12624333 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848488.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848488"; exon_number 4; exon_id "ENSE00004278032.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12625317 12626718 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848488.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848488"; exon_number 5; exon_id "ENSE00004278036.1"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA transcript 12602329 12629201 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848485.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848485"; level 2; tag "basic"; tag "TAGENE"; +chr22 HAVANA exon 12602329 12602527 . + . gene_id "ENSG00000310236.1"; transcript_id "ENST00000848485.1"; gene_type "lncRNA"; gene_name "ENSG00000310236"; transcript_type "lncRNA"; transcript_name "ENST00000848485"; exon_number 1; exon_id "ENSE00004278028.1"; level 2; tag "basic"; tag "TAGENE"; diff --git a/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz b/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz new file mode 100644 index 0000000..93422c9 Binary files /dev/null and b/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz differ diff --git a/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz.tbi b/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz.tbi new file mode 100644 index 0000000..33d8bce Binary files /dev/null and b/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz.tbi differ diff --git a/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_regions.bed b/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_regions.bed new file mode 100644 index 0000000..70a3dff --- /dev/null +++ b/test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_regions.bed @@ -0,0 +1,200 @@ +chr20 81335 101267 +chr20 101308 102558 +chr20 102684 105312 +chr20 105417 112950 +chr20 113052 115904 +chr20 116012 128466 +chr20 128568 132145 +chr20 132167 135832 +chr20 135853 140801 +chr20 140931 148813 +chr20 149421 154077 +chr20 154179 154423 +chr20 154530 156826 +chr20 156986 157876 +chr20 157988 159235 +chr20 159337 162881 +chr20 162909 173697 +chr20 173718 177284 +chr20 177386 191675 +chr20 191778 199088 +chr20 199190 201881 +chr20 201984 212989 +chr20 213023 214957 +chr20 214984 231863 +chr20 231886 234093 +chr20 234196 236845 +chr20 237010 240426 +chr20 240528 243767 +chr20 243884 245392 +chr20 245525 251319 +chr20 251421 255305 +chr20 255407 256957 +chr20 257095 258716 +chr20 258821 262147 +chr20 262249 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T T]10:36119127] 2491.83 PASS AS=1;ASC=506M1X;ASQ=932.36;ASRP=79;ASSR=44;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm34-10701,asm686-4441,asm687-5527,asm687-5573;BEIDH=507,145,0,0;BEIDL=0,212,67,2;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=16.56;BSC=1;BSCQ=16.56;BUM=0;BUMQ=0.00;BVF=0;CAS=1;CASQ=708.36;CQ=2474.65;EVENT=gridss34ff_681;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss34ff_681h;MQ=60.00;MQN=60.00;MQX=60.00;PURPLE_AF=0.277,0.276;PURPLE_CN=2.84,2.71;PURPLE_CN_CHANGE=0.833,0.753;PURPLE_JCN=0.767;RAS=2;RASQ=449.56;REF=98;REFG=CAAGGAGATCTTAGTATGTTA;REFPAIR=74;REMOTE_LINKED_BY=asm686-4441/145,asm34-10701/507;RP=5;RPQ=80.35;SB=0.5833333;SC=506M1X;SR=17;SRQ=321.20;SVTYPE=BND;TAF=0.275;VF=46 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:26:25:0:0.00:0:0.00:0 .:932.36:79:44:0:0.00:0:0.00:0.00:0:0:16.56:1:16.56:0:0.00:0:708.36:0:0.00:2491.83:449.56:72:49:5:80.35:17:321.20:46 +1 118516186 gridss47fb_486o T T[1:118516222[ 3697.49 PASS AS=1;ASC=1X;ASQ=1247.21;ASRP=0;ASSR=68;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm47-11854,asm47-3490;BEIDH=0,0;BEIDL=0,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=123.88;BSC=6;BSCQ=94.96;BUM=1;BUMQ=28.92;BVF=1;CAS=0;CASQ=0.00;CQ=3697.49;EVENT=gridss47fb_486;IC=23;IHOMPOS=0,0;IQ=1082.23;LOCAL_LINKED_BY=.;MATEID=gridss47fb_486h;MQ=60.00;MQN=60.00;MQX=60.00;PURPLE_AF=0.412,0.424;PURPLE_CN=2.00,2.02;PURPLE_CN_CHANGE=0.833,0.849;PURPLE_JCN=0.841;RAS=1;RASQ=1281.99;REF=86;REFG=ATTCTGCTTCTGTTAGAGAGA;REFPAIR=68;REMOTE_LINKED_BY=.;RP=1;RPQ=16.05;SB=0.23762377;SC=147M414D116M1X;SR=4;SRQ=70.01;SVTYPE=BND;TAF=0.408;VF=42 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:28.92:0:0.00:1:28.92:1:0.00:0:0.00:0.00:0.00:25:27:0:0.00:0:0.00:0 .:1247.21:0:68:0:0.00:0:0.00:0.00:0:0:94.96:6:94.96:0:0.00:0:0.00:23:1082.23:3697.49:1281.99:61:41:1:16.05:4:70.01:42 +1 118516222 gridss47fb_486h T ]1:118516186]T 3697.49 PASS AS=1;ASC=1X;ASQ=1281.99;ASRP=0;ASSR=68;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm47-11854,asm47-3490;BEIDH=0,0;BEIDL=0,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=129.74;BSC=8;BSCQ=129.74;BUM=0;BUMQ=0.00;BVF=0;CAS=0;CASQ=0.00;CQ=3697.49;EVENT=gridss47fb_486;IC=23;IHOMPOS=0,0;IQ=1082.23;LOCAL_LINKED_BY=.;MATEID=gridss47fb_486o;MQ=60.00;MQN=60.00;MQX=60.00;PURPLE_AF=0.424,0.412;PURPLE_CN=2.02,2.00;PURPLE_CN_CHANGE=0.849,0.833;PURPLE_JCN=0.841;RAS=1;RASQ=1247.21;REF=84;REFG=CACATGGACATTTTATTCAAA;REFPAIR=64;REMOTE_LINKED_BY=.;RP=1;RPQ=16.05;SB=0.26213592;SC=1X112M103D151M;SR=4;SRQ=70.01;SVTYPE=BND;TAF=0.420;VF=42 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:26:24:0:0.00:0:0.00:0 .:1281.99:0:68:0:0.00:0:0.00:0.00:0:0:129.74:8:129.74:0:0.00:0:0.00:23:1082.23:3697.49:1247.21:58:40:1:16.05:4:70.01:42 +1 142621506 gridss57bb_71o T [3:75831689[T 408.46 PON 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.:353.60:4:14:0:0.00:0:0.00:0.00:0:0:829.59:24:381.66:17:447.93:26:0.00:0:0.00:408.46:0.00:548:464:0:0.00:3:54.86:18 +1 145136259 gridss58f_1316b T TTTTTTTTTTTTTTTTTTTTT. 1733.46 PON AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=3;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=855.23;BASRP=25;BASSR=10;BEID=asm58-2220,asm58-2222,asm58-2233;BEIDH=-1,-1,-1;BEIDL=0,0,0;BMQ=43.48;BMQN=21.00;BMQX=60.00;BQ=1748.28;BSC=11;BSCQ=171.15;BUM=26;BUMQ=721.90;BVF=37;CAS=0;CASQ=0.00;CQ=3212.44;EVENT=gridss58f_1316;IC=0;IQ=0.00;LOCAL_LINKED_BY=.;PURPLE_AF=0.112;PURPLE_CN=3.92;PURPLE_CN_CHANGE=0.00;PURPLE_JCN=0.437;RAS=0;RASQ=0.00;REF=265;REFG=TGCTGCTTTATACAACAGTGT;REFPAIR=107;REMOTE_LINKED_BY=.;RP=0;RPQ=0.00;SB=0.35714287;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.111;VF=0 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:14.81:1:14.81:0:0.00:1:0.00:0:0.00:0.00:0.00:54:31:0:0.00:0:0.00:0 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GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:35:33:0:0.00:0:0.00:0 .:698.28:38:35:0:0.00:0:0.00:0.00:0:0:133.10:1:16.33:4:116.77:2:0.00:0:0.00:1928.90:590.98:112:84:21:337.47:16:302.17:33 +1 208014820 gridss83fb_413h G ]1:207981231]G 1928.90 PASS AS=1;ASC=1X3D385M;ASQ=590.98;ASRP=38;ASSR=35;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm83-16355,asm83-2653;BEIDH=0,0;BEIDL=580,409;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=90.07;BSC=2;BSCQ=31.69;BUM=2;BUMQ=58.39;BVF=1;CAS=0;CASQ=0.00;CIPOS=-2,2;CIRPOS=-2,2;CQ=1896.76;EVENT=gridss83fb_413;HOMLEN=4;HOMSEQ=GAGG;IC=0;IHOMPOS=-2,2;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss83fb_413o;MQ=59.62;MQN=37.00;MQX=60.00;PURPLE_AF=0.224,0.145;PURPLE_CN=3.93,3.92;PURPLE_CN_CHANGE=0.964,0.952;PURPLE_JCN=0.724;RAS=1;RASQ=698.28;REF=102;REFG=GGCTCTGGGAGGAATTCATAG;REFPAIR=42;REMOTE_LINKED_BY=.;RP=21;RPQ=337.47;SB=0.24528302;SC=1X388M6D151M;SR=16;SRQ=302.17;SVTYPE=BND;TAF=0.223;VF=33 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:20:9:0:0.00:0:0.00:0 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GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:43:25:0:0.00:0:0.00:0 .:1318.96:94:86:0:0.00:0:0.00:0.00:0:0:662.55:35:604.16:2:58.39:16:0.00:0:0.00:4949.07:1976.39:139:99:65:1044.55:28:609.17:97 +1 224782795 gridss89fb_2141o C CCTATAGTAGAACTTCTTTT[1:224786034[ 6260.30 PASS AS=1;ASC=598M1X;ASQ=2480.46;ASRP=197;ASSR=65;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm89-15604,asm89-32549;BEIDH=618,618;BEIDL=0,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=892.28;BSC=38;BSCQ=687.93;BUM=7;BUMQ=204.35;BVF=4;CAS=0;CASQ=0.00;CQ=6212.09;EVENT=gridss89fb_2141;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss89fb_2141h;MQ=58.34;MQN=24.00;MQX=60.00;PURPLE_AF=0.357,0.342;PURPLE_CN=5.95,6.01;PURPLE_CN_CHANGE=1.96,2.02;PURPLE_JCN=2.09;RAS=1;RASQ=1994.70;REF=169;REFG=TGTTGTCAGGCTGGAGTGCAG;REFPAIR=119;REMOTE_LINKED_BY=.;RP=96;RPQ=1542.72;SB=0.6230769;SC=598M1X;SR=12;SRQ=242.42;SVTYPE=BND;TAF=0.356;VF=126 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:33:27:0:0.00:0:0.00:0 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AS=0;ASC=1X51M154D493M;ASQ=0.00;ASRP=0;ASSR=12;BA=0;BANRP=13;BANRPQ=208.91;BANSR=12;BANSRQ=207.98;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm464-17210,asm464-17224;BEIDH=52,493;BEIDL=0,0;BMQ=57.54;BMQN=36.00;BMQX=60.00;BQ=671.62;BSC=26;BSCQ=613.51;BUM=2;BUMQ=58.11;BVF=27;CAS=0;CASQ=0.00;CQ=416.89;EVENT=gridss94bb_186;IC=0;IHOMPOS=0,7;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss94bb_186h;MQ=35.52;MQN=20.00;MQX=60.00;PURPLE_AF=0.056,0.087;PURPLE_CN=3.89,2.87;PURPLE_CN_CHANGE=0.00,0.00;PURPLE_JCN=0.234;RAS=2;RASQ=207.98;REF=115;REFG=GAAGGGAGGAAGGAGGGAGGG;REFPAIR=158;REMOTE_LINKED_BY=dsb1358;RP=13;RPQ=208.91;SB=0.24;SC=1X51M154D493M;SR=12;SRQ=207.98;SVTYPE=BND;TAF=0.056;VF=13 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:153.16:6:124.25:1:28.92:7:0.00:0:0.00:0.00:0.00:19:33:0:0.00:0:0.00:0 .:0.00:0:12:13:208.91:12:207.98:0.00:0:0:518.46:20:489.27:1:29.19:20:0.00:0:0.00:624.88:207.98:96:125:13:208.91:12:207.98:13 +1 236345211 gridss94f_7049b T TTTTTTTTTTTTTAAATTAAATATTTTTTTTTTTTTTTTACCTTTTTTTTTTTTTTTTTTTTT. 1047.25 PON AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=1;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=519.67;BASRP=1;BASSR=28;BEALN=14:68377123|-|21M3I23M15S|0;BEID=asm94-11181;BEIDH=-1;BEIDL=3;BMQ=55.10;BMQN=24.00;BMQX=60.00;BQ=1047.25;BSC=28;BSCQ=498.39;BUM=1;BUMQ=29.19;BVF=30;CAS=0;CASQ=0.00;CQ=1110.83;EVENT=gridss94f_7049;IC=0;INSRMP=0.682;INSRMRC=SINE/Alu;INSRMRO=-;INSRMRT=AluYc;IQ=0.00;LOCAL_LINKED_BY=.;PURPLE_AF=0.118;PURPLE_CN=3.89;PURPLE_CN_CHANGE=0.00;PURPLE_JCN=0.458;RAS=0;RASQ=0.00;REF=157;REFG=TTTTTTTTTTTGAGACGGAGT;REFPAIR=116;REMOTE_LINKED_BY=.;RP=0;RPQ=0.00;SB=0.75;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.117;VF=0 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:31:15:0:0.00:0:0.00:0 .:0.00:0:0:0:0.00:0:0.00:519.67:1:28:1047.25:28:498.39:1:29.19:30:0.00:0:0.00:0.00:0.00:126:101:0:0.00:0:0.00:0 +1 239575617 gridss95ff_672o T TCCCCCACCTCTTTCCTCCCTCCCTGTCTTCCCTTCCTCTTCCCCA]15:44497339] 658.15 PON AS=0;ASC=46M1X;ASQ=0.00;ASRP=0;ASSR=10;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm942-154;BEIDH=4;BEIDL=162;BMQ=58.81;BMQN=30.00;BMQX=60.00;BQ=5486.81;BSC=91;BSCQ=2019.76;BUM=119;BUMQ=3467.06;BVF=165;CAS=0;CASQ=0.00;CQ=658.15;EVENT=gridss95ff_672;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss95ff_672h;MQ=38.04;MQN=20.00;MQX=60.00;PURPLE_AF=0.362,0.142;PURPLE_CN=3.89,2.01;PURPLE_CN_CHANGE=0.00,0.00;PURPLE_JCN=0.847;RAS=1;RASQ=215.08;REF=39;REFG=CTCCCTTCCTTTCTTCTTCCT;REFPAIR=5;REMOTE_LINKED_BY=.;RP=18;RPQ=289.26;SB=0.559633;SC=512M29D46M1X;SR=7;SRQ=153.81;SVTYPE=BND;TAF=0.360;VF=18 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:1279.44:24:556.54:25:722.90:36:0.00:0:0.00:0.00:0.00:9:3:0:0.00:0:0.00:0 .:0.00:0:10:0:0.00:0:0.00:0.00:0:0:4207.37:67:1463.21:94:2744.16:129:0.00:0:0.00:658.15:215.08:30:2:18:289.26:7:153.81:18 +2 2824187 gridss100fb_2279o A A[10:102074730[ 420.46 PON AS=0;ASC=302M1X20N1X;ASQ=0.00;ASRP=0;ASSR=12;BA=0;BANRP=3;BANRPQ=48.21;BANSR=8;BANSRQ=150.88;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm713-20777,asm713-20824;BEIDH=65,243;BEIDL=0,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=58.39;BSC=0;BSCQ=0.00;BUM=2;BUMQ=58.39;BVF=2;CAS=0;CASQ=0.00;CIPOS=-10,11;CIRPOS=-10,11;CQ=404.39;EVENT=gridss100fb_2279;HOMLEN=21;HOMSEQ=GAAGGAAGGAAGGAAGGAAGG;IC=0;IHOMPOS=-10,11;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss100fb_2279h;MQ=45.77;MQN=25.00;MQX=60.00;PURPLE_AF=0.095,0.120;PURPLE_CN=3.01,2.01;PURPLE_CN_CHANGE=0.00,0.00;PURPLE_JCN=0.263;RAS=2;RASQ=221.37;REF=101;REFG=GGAAGGAAGGAAGGAAGGAAG;REFPAIR=94;REMOTE_LINKED_BY=.;RP=3;RPQ=48.21;SB=0.85;SC=302M1X20N1X;SR=8;SRQ=150.88;SVTYPE=BND;TAF=0.094;VF=15 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:23:27:0:0.00:0:0.00:0 .:0.00:0:12:3:48.21:8:150.88:0.00:0:0:58.39:0:0.00:2:58.39:2:0.00:0:0.00:420.46:221.37:78:67:3:48.21:8:150.88:15 +2 10965380 gridss104fb_579o C C[2:10965415[ 2664.93 PON AS=2;ASC=1X20N1X;ASQ=974.45;ASRP=0;ASSR=64;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm104-18346,asm104-3657,asm104-3658;BEIDH=0,0,0;BEIDL=0,0,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=220.14;BSC=12;BSCQ=190.94;BUM=1;BUMQ=29.19;BVF=3;CAS=0;CASQ=0.00;CIPOS=-10,11;CIRPOS=-10,11;CQ=2804.19;EVENT=gridss104fb_579;HOMLEN=21;HOMSEQ=TCTCTCTCTCTGTCTCTCTCT;IC=16;IHOMPOS=-10,17;IQ=744.53;LOCAL_LINKED_BY=dsb346;MATEID=gridss104fb_579h;MQ=59.48;MQN=37.00;MQX=60.00;PURPLE_AF=0.343,0.380;PURPLE_CN=3.01,3.01;PURPLE_CN_CHANGE=0.00,0.00;PURPLE_JCN=1.09;RAS=1;RASQ=1012.98;REF=98;REFG=CTCTCTCTCTCTGTCTCTCTC;REFPAIR=105;REMOTE_LINKED_BY=.;RP=0;RPQ=0.00;SB=0.41666666;SC=82M1X20N1X;SR=4;SRQ=72.24;SVTYPE=BND;TAF=0.341;VF=44 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:46.42:0:2:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:1:46.42:139.26:46.42:15:28:0:0.00:0:0.00:1 .:928.03:0:62:0:0.00:0:0.00:0.00:0:0:220.14:12:190.94:1:29.19:3:0.00:15:698.10:2664.93:966.56:83:77:0:0.00:4:72.24:43 +2 10965415 gridss104fb_579h T ]2:10965380]T 2664.93 PON AS=1;ASC=1X6N1X;ASQ=1012.98;ASRP=0;ASSR=64;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm104-18346,asm104-3657,asm104-3658;BEIDH=0,0,0;BEIDL=0,0,0;BQ=0.00;BSC=0;BSCQ=0.00;BUM=0;BUMQ=0.00;BVF=0;CAS=0;CASQ=0.00;CIPOS=-10,11;CIRPOS=-10,11;CQ=2804.19;EVENT=gridss104fb_579;HOMLEN=21;HOMSEQ=TCTCTCTCTCTGTCTCTCTCT;IC=16;IHOMPOS=-10,17;IQ=744.53;LOCAL_LINKED_BY=.;MATEID=gridss104fb_579o;MQ=59.48;MQN=37.00;MQX=60.00;PURPLE_AF=0.380,0.343;PURPLE_CN=3.01,3.01;PURPLE_CN_CHANGE=0.00,0.00;PURPLE_JCN=1.09;RAS=2;RASQ=974.45;REF=86;REFG=TCTCTCTCTCTGTCTCTCTCT;REFPAIR=99;REMOTE_LINKED_BY=dsb346;RP=0;RPQ=0.00;SB=0.41666666;SC=1X6N1X100M;SR=4;SRQ=72.24;SVTYPE=BND;TAF=0.377;VF=44 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:46.42:0:2:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:1:46.42:139.26:46.42:15:22:0:0.00:0:0.00:1 .:966.56:0:62:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:15:698.10:2664.93:928.03:71:77:0:0.00:4:72.24:43 +2 63799860 gridss125f_2408b A AAAAAAAAAAAAAAAAGTTGGAAACCAAAAATCACAGCCAAGGTATTAATGAGGGCAAAAAAATGAAAATTTTGAAATTTGTAAAAAAAAAT. 1007.55 PON AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=1;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=537.58;BASRP=9;BASSR=13;BEID=asm125-3862;BEIDH=-1;BEIDL=0;BMQ=55.05;BMQN=40.00;BMQX=60.00;BQ=1007.55;BSC=11;BSCQ=207.23;BUM=9;BUMQ=262.74;BVF=22;CAS=0;CASQ=0.00;CQ=1036.75;EVENT=gridss125f_2408;IC=0;IQ=0.00;LOCAL_LINKED_BY=.;PURPLE_AF=0.124;PURPLE_CN=3.01;PURPLE_CN_CHANGE=0.00;PURPLE_JCN=0.373;RAS=0;RASQ=0.00;REF=104;REFG=AAAAAAAAAAAGTTGGACAGC;REFPAIR=100;REMOTE_LINKED_BY=.;RP=0;RPQ=0.00;SB=1.0;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.123;VF=0 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:25:22:0:0.00:0:0.00:0 .:0.00:0:0:0:0.00:0:0.00:537.58:9:13:1007.55:11:207.23:9:262.74:22:0.00:0:0.00:0.00:0.00:79:78:0:0.00:0:0.00:0 +2 212123717 gridss184fb_1050o G GAGGGAAA[20:41696744[ 408.91 PON AS=2;ASC=1X;ASQ=276.42;ASRP=6;ASSR=9;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm184-6986,asm184-7005;BEIDH=82,2;BEIDL=0,0;BMQ=40.00;BMQN=40.00;BMQX=40.00;BQ=18.47;BSC=1;BSCQ=18.47;BUM=0;BUMQ=0.00;BVF=1;CAS=0;CASQ=0.00;CQ=408.91;EVENT=gridss184fb_1050;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss184fb_1050h;MQ=39.40;MQN=20.00;MQX=60.00;RAS=0;RASQ=0.00;REF=58;REFG=AGGGAGGGAGGGAGGGAAGAA;REFPAIR=126;REMOTE_LINKED_BY=dsb3139;RP=7;RPQ=112.49;SB=1.0;SC=70M1X;SR=1;SRQ=20.00;SVTYPE=BND;TAF=0.100;VF=16 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:13:27:0:0.00:0:0.00:0 .:276.42:6:9:0:0.00:0:0.00:0.00:0:0:18.47:1:18.47:0:0.00:1:0.00:0:0.00:408.91:0.00:45:99:7:112.49:1:20.00:16 +3 24565107 gridss207bb_4o C [3:24566181[C 13865.59 PASS AS=1;ASC=1X2N1X604M;ASQ=4647.29;ASRP=326;ASSR=233;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm207-22210,asm207-22219;BEIDH=0,608;BEIDL=566,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=235.27;BSC=15;BSCQ=235.27;BUM=0;BUMQ=0.00;BVF=0;CAS=0;CASQ=0.00;CIPOS=-1,2;CIRPOS=-2,1;CQ=13801.31;EVENT=gridss207bb_4;HOMLEN=3;HOMSEQ=TCA;IC=0;IHOMPOS=-1,2;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss207bb_4h;MQ=60.00;MQN=60.00;MQX=60.00;PURPLE_AF=0.615,0.357;PURPLE_CN=6.02,10.04;PURPLE_CN_CHANGE=4.02,4.02;PURPLE_JCN=3.64;RAS=1;RASQ=4790.21;REF=115;REFG=AAGACACAATCACAGTTTCCC;REFPAIR=82;REMOTE_LINKED_BY=.;RP=164;RPQ=2635.48;SB=0.4869565;SC=1X2N1X604M;SR=97;SRQ=1792.61;SVTYPE=BND;TAF=0.613;VF=222 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:32:25:0:0.00:0:0.00:0 .:4647.29:326:233:0:0.00:0:0.00:0.00:0:0:235.27:15:235.27:0:0.00:0:0.00:0:0.00:13865.59:4790.21:83:57:164:2635.48:97:1792.61:222 +3 24566181 gridss207bb_4h A [3:24565107[A 13865.59 PASS AS=1;ASC=1X2D566M;ASQ=4790.21;ASRP=326;ASSR=233;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm207-22210,asm207-22219;BEIDH=566,0;BEIDL=0,608;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=378.19;BSC=24;BSCQ=378.19;BUM=0;BUMQ=0.00;BVF=0;CAS=0;CASQ=0.00;CIPOS=-2,1;CIRPOS=-1,2;CQ=13801.31;EVENT=gridss207bb_4;HOMLEN=3;HOMSEQ=TGA;IC=0;IHOMPOS=-2,1;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss207bb_4o;MQ=60.00;MQN=60.00;MQX=60.00;PURPLE_AF=0.357,0.615;PURPLE_CN=10.04,6.02;PURPLE_CN_CHANGE=4.02,4.02;PURPLE_JCN=3.64;RAS=1;RASQ=4647.29;REF=264;REFG=CTTCTCTTTGAGCAGAGCTAT;REFPAIR=192;REMOTE_LINKED_BY=.;RP=164;RPQ=2635.48;SB=0.5084746;SC=1X568M;SR=97;SRQ=1792.61;SVTYPE=BND;TAF=0.356;VF=222 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:27:27:0:0.00:0:0.00:0 .:4790.21:326:233:0:0.00:0:0.00:0.00:0:0:378.19:24:378.19:0:0.00:0:0.00:0:0.00:13865.59:4647.29:237:165:164:2635.48:97:1792.61:222 +3 24854939 gridss207f_1643b T TTCTTTCTTTCTT. 3185.68 PON AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=3;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=2591.48;BASRP=19;BASSR=73;BEID=asm207-2723,asm207-2780,asm207-2784;BEIDH=-1,-1,-1;BEIDL=0,0,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=3242.31;BSC=6;BSCQ=96.16;BUM=19;BUMQ=554.67;BVF=91;CAS=0;CASQ=0.00;CQ=3348.08;EVENT=gridss207f_1643;IC=0;IQ=0.00;LOCAL_LINKED_BY=.;PURPLE_AF=0.152;PURPLE_CN=10.04;PURPLE_CN_CHANGE=0.00;PURPLE_JCN=1.53;RAS=0;RASQ=0.00;REF=299;REFG=CTTTCTTTCTTCTTTCCTTCT;REFPAIR=234;REMOTE_LINKED_BY=.;RP=0;RPQ=0.00;SB=0.3625;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.152;VF=0 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:56.62:0:2:56.62:0:0.00:0:0.00:2:0.00:0:0.00:0.00:0.00:13:24:0:0.00:0:0.00:0 .:0.00:0:0:0:0.00:0:0.00:2534.86:19:71:3185.68:6:96.16:19:554.67:89:0.00:0:0.00:0.00:0.00:286:210:0:0.00:0:0.00:0 +3 25331584 gridss207b_4627b G .AATCACCGAATAGAATCGAATGGAACAATCATCGAATGGACTCAAATGGAATTATCCTCAAATGGAATGGAATGGAATTATTGAATGCAATCGAAAGGAATTATCGAATGCAATCGAATAGAATCATCGAATGGACTCGAATGGAATCATCGAATGGAATGGAATGGAACAGTCAATGAACTCGAATGGAATCATCATTGAATGGAATCGAATGGAATCATCGAGTGGAATCGAATGGAATTATGATCAAATGGAATCGAATGTAATCATCATCAAATGGAATCAAAAATAACCATCATCAATTGGTATTGAATGGAATTGTCATCAAATGGAATTCAAAGGAATCATCATCAAATGGAACCGAATGGAATCCTCATTGAATGGAAATGAAAGGGGTCATCATCTAATGGAATCGCATGGAATCATCATCAAATGGAATCGAATGTAATCTTCATCAAATGGAATCTAATGGAATCATTGAACAGAATTGAATGGAATCGTCATCGAATGAATTGAATGCAATCATCGAATGGTCTCGAATGGAATCATCTTCTAATGTAAAG 7033.79 PASS AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=1;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=3458.51;BASRP=92;BASSR=43;BEALN=10:42395911|+|428M1I119M14S|15;BEID=asm207-30084;BEIDH=-1;BEIDL=562;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=7033.79;BSC=43;BSCQ=772.73;BUM=96;BUMQ=2802.55;BVF=111;CAS=0;CASQ=0.00;CQ=7015.16;EVENT=gridss207b_4627;IC=0;INSRMP=1.00;INSRMRC=Satellite;INSRMRO=-;INSRMRT=HSATII;IQ=0.00;LOCAL_LINKED_BY=.;PURPLE_AF=0.149;PURPLE_CN=12.06;PURPLE_CN_CHANGE=2.02;PURPLE_JCN=1.80;RAS=0;RASQ=0.00;REF=424;REFG=TTAGGCTAATGAAGCATTGAG;REFPAIR=258;REMOTE_LINKED_BY=.;RP=0;RPQ=0.00;SB=0.3488372;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.149;VF=0 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:32:16:0:0.00:0:0.00:0 .:0.00:0:0:0:0.00:0:0.00:3458.51:92:43:7033.79:43:772.73:96:2802.55:111:0.00:0:0.00:0.00:0.00:392:242:0:0.00:0:0.00:0 +3 25400602 gridss207fb_1147o G GTGAATCCATCA[12:72666892[ 5269.90 PASS AS=1;ASC=651M1X;ASQ=1763.36;ASRP=172;ASSR=73;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm207-8593,asm207-8594,asm697-1654,asm810-16037;BEIDH=567,809,200,663;BEIDL=0,1003,394,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=339.77;BSC=14;BSCQ=223.00;BUM=4;BUMQ=116.77;BVF=9;CAS=2;CASQ=913.04;CQ=5253.83;EVENT=gridss207fb_1147;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss207fb_1147h;MQ=56.25;MQN=26.00;MQX=60.00;PURPLE_AF=0.153,0.332;PURPLE_CN=12.06,4.76;PURPLE_CN_CHANGE=2.00,1.75;PURPLE_JCN=1.72;RAS=1;RASQ=1492.69;REF=385;REFG=ATCTGGTTCTGGGCTTTTTTT;REFPAIR=283;REMOTE_LINKED_BY=asm697-1654/200,asm207-8594/809,asm207-8593/567;RP=41;RPQ=658.87;SB=0.5693069;SC=651M1X;SR=22;SRQ=441.93;SVTYPE=BND;TAF=0.153;VF=111 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:23:30:0:0.00:0:0.00:0 .:1763.36:172:73:0:0.00:0:0.00:0.00:0:0:339.77:14:223.00:4:116.77:9:913.04:0:0.00:5269.90:1492.69:362:253:41:658.87:22:441.93:111 +3 25401059 gridss207fb_1150o G G[10:60477224[ 4568.11 PASS AS=1;ASC=607M1X;ASQ=1477.23;ASRP=150;ASSR=67;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm207-8593,asm207-8594,asm697-10757,asm810-5102;BEIDH=751,609,608,184;BEIDL=950,0,0,383;BMQ=57.50;BMQN=20.00;BMQX=60.00;BQ=273.19;BSC=15;BSCQ=244.00;BUM=1;BUMQ=29.19;BVF=0;CAS=2;CASQ=676.28;CQ=4535.97;EVENT=gridss207fb_1150;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss207fb_1150h;MQ=57.03;MQN=24.00;MQX=60.00;PURPLE_AF=0.176,0.432;PURPLE_CN=10.06,3.64;PURPLE_CN_CHANGE=2.08,1.66;PURPLE_JCN=1.67;RAS=1;RASQ=1515.90;REF=301;REFG=TGTGATGTTAGAGTGTTGATT;REFPAIR=218;REMOTE_LINKED_BY=asm207-8593/751,asm207-8594/609,asm810-5102/184;RP=46;RPQ=739.22;SB=0.4054054;SC=607M1X;SR=9;SRQ=159.49;SVTYPE=BND;TAF=0.176;VF=99 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:27:27:0:0.00:0:0.00:0 .:1477.23:150:67:0:0.00:0:0.00:0.00:0:0:273.19:15:244.00:1:29.19:0:676.28:0:0.00:4568.11:1515.90:274:191:46:739.22:9:159.49:99 +3 26431918 gridss207bb_1124o G [6:26194040[G 6695.99 PASS AS=0;ASC=1X1N1X749M;ASQ=0.00;ASRP=187;ASSR=74;BA=0;BANRP=53;BANRPQ=851.71;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm435-14858,asm435-30703;BEIDH=378,752;BEIDL=455,0;BMQ=54.56;BMQN=37.00;BMQX=60.00;BQ=1048.27;BSC=11;BSCQ=172.47;BUM=30;BUMQ=875.80;BVF=41;CAS=1;CASQ=1711.53;CIPOS=-1,1;CIRPOS=-1,1;CQ=6663.85;EVENT=gridss207bb_1124;HOMLEN=2;HOMSEQ=TG;IC=0;IHOMPOS=-1,1;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss207bb_1124h;MQ=59.73;MQN=44.00;MQX=60.00;PURPLE_AF=0.300,0.450;PURPLE_CN=11.84,7.35;PURPLE_CN_CHANGE=3.85,3.48;PURPLE_JCN=3.43;RAS=1;RASQ=4132.75;REF=286;REFG=AGCCAGGTGTGGGATATAGTC;REFPAIR=211;REMOTE_LINKED_BY=asm435-14858/378;RP=53;RPQ=851.71;SB=0.50427353;SC=1X1N1X749M;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.299;VF=189 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:37:16:0:0.00:0:0.00:0 .:0.00:187:74:53:851.71:0:0.00:0.00:0:0:1048.27:11:172.47:30:875.80:41:1711.53:0:0.00:6695.99:4132.75:249:195:53:851.71:0:0.00:189 +3 26663921 gridss207ff_1240o G G]3:26664499] 13426.48 PASS AS=1;ASC=642M2X;ASQ=4485.73;ASRP=330;ASSR=223;BA=0;BANRP=2;BANRPQ=32.14;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm207-19992,asm207-19993;BEIDH=580,0;BEIDL=0,581;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=587.96;BSC=25;BSCQ=413.08;BUM=6;BUMQ=174.88;BVF=6;CAS=0;CASQ=0.00;CIPOS=0,1;CIRPOS=-1,0;CQ=13426.48;EVENT=gridss207ff_1240;HOMLEN=1;HOMSEQ=G;IC=0;IHOMPOS=0,1;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss207ff_1240h;MQ=60.00;MQN=60.00;MQX=60.00;PURPLE_AF=0.335,0.468;PURPLE_CN=11.84,7.92;PURPLE_CN_CHANGE=3.92,3.92;PURPLE_JCN=3.83;RAS=1;RASQ=4812.11;REF=327;REFG=CCCCCAAGGAGGGCAATCAAT;REFPAIR=215;REMOTE_LINKED_BY=.;RP=165;RPQ=2651.55;SB=0.49847096;SC=642M2X;SR=79;SRQ=1477.09;SVTYPE=BND;TAF=0.334;VF=244 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:28.92:0:0.00:1:28.92:1:0.00:0:0.00:0.00:0.00:31:25:0:0.00:0:0.00:0 .:4485.73:330:223:2:32.14:0:0.00:0.00:0:0:559.05:25:413.08:5:145.97:5:0.00:0:0.00:13426.48:4812.11:296:190:165:2651.55:79:1477.09:244 +3 26664499 gridss207ff_1240h C C]3:26663921] 13426.48 PASS AS=1;ASC=581M1X;ASQ=4812.11;ASRP=330;ASSR=223;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm207-19992,asm207-19993;BEIDH=0,581;BEIDL=580,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=651.33;BSC=41;BSCQ=651.33;BUM=0;BUMQ=0.00;BVF=0;CAS=0;CASQ=0.00;CIPOS=-1,0;CIRPOS=0,1;CQ=13426.48;EVENT=gridss207ff_1240;HOMLEN=1;HOMSEQ=C;IC=0;IHOMPOS=-1,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss207ff_1240o;MQ=60.00;MQN=60.00;MQX=60.00;PURPLE_AF=0.468,0.335;PURPLE_CN=7.92,11.84;PURPLE_CN_CHANGE=3.92,3.92;PURPLE_JCN=3.83;RAS=1;RASQ=4485.73;REF=204;REFG=CCGCGCCACGCACTGCCTGCG;REFPAIR=139;REMOTE_LINKED_BY=.;RP=165;RPQ=2651.55;SB=0.41982508;SC=665M1X;SR=79;SRQ=1477.09;SVTYPE=BND;TAF=0.467;VF=244 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:33:31:0:0.00:0:0.00:0 .:4812.11:330:223:0:0.00:0:0.00:0.00:0:0:651.33:41:651.33:0:0.00:0:0.00:0:0.00:13426.48:4485.73:171:108:165:2651.55:79:1477.09:244 +3 60132754 gridss221fb_469o T T[3:60204543[ 3145.32 PASS AS=2;ASC=553M1X;ASQ=1085.88;ASRP=78;ASSR=49;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm221-16874,asm221-2935,asm221-2943;BEIDH=554,300,2;BEIDL=0,0,0;BMQ=60.00;BMQN=60.00;BMQX=60.00;BQ=125.00;BSC=6;BSCQ=95.81;BUM=1;BUMQ=29.19;BVF=1;CAS=0;CASQ=0.00;CQ=3127.01;EVENT=gridss221fb_469;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss221fb_469h;MQ=56.46;MQN=25.00;MQX=60.00;PURPLE_AF=0.232,0.230;PURPLE_CN=4.00,3.93;PURPLE_CN_CHANGE=1.14,1.07;PURPLE_JCN=0.917;RAS=1;RASQ=1069.36;REF=124;REFG=CGCAATCCTTTATTTTCCTTT;REFPAIR=81;REMOTE_LINKED_BY=.;RP=39;RPQ=626.73;SB=0.5135135;SC=553M1X;SR=19;SRQ=363.34;SVTYPE=BND;TAF=0.231;VF=49 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:20:22:0:0.00:0:0.00:0 .:1085.88:78:49:0:0.00:0:0.00:0.00:0:0:125.00:6:95.81:1:29.19:1:0.00:0:0.00:3145.32:1069.36:104:59:39:626.73:19:363.34:49 +3 60204543 gridss221fb_469h T ]3:60132754]T 3145.32 PASS AS=1;ASC=1X514M;ASQ=1069.36;ASRP=78;ASSR=49;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm221-16874,asm221-2935,asm221-2943;BEIDH=0,0,0;BEIDL=554,300,2;BMQ=44.17;BMQN=25.00;BMQX=60.00;BQ=108.48;BSC=5;BSCQ=79.28;BUM=1;BUMQ=29.19;BVF=1;CAS=0;CASQ=0.00;CQ=3127.01;EVENT=gridss221fb_469;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=.;MATEID=gridss221fb_469o;MQ=56.46;MQN=25.00;MQX=60.00;PURPLE_AF=0.230,0.232;PURPLE_CN=3.93,4.00;PURPLE_CN_CHANGE=1.07,1.14;PURPLE_JCN=0.917;RAS=2;RASQ=1085.88;REF=128;REFG=GTGACATAAATGAGGTTTGAA;REFPAIR=91;REMOTE_LINKED_BY=.;RP=39;RPQ=626.73;SB=0.46575344;SC=1X514M;SR=19;SRQ=363.34;SVTYPE=BND;TAF=0.229;VF=49 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF 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GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:31:21:0:0.00:0:0.00:0 .:1297.58:84:69:0:0.00:0:0.00:0.00:0:0:181.48:6:93.90:3:87.58:3:0.00:0:0.00:3817.42:1316.16:127:67:42:674.94:28:528.74:65 +3 61013214 gridss221fb_1053h C ]3:60872124]C 3817.42 PASS 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.:2582.32:0:133:0:0.00:0:0.00:0.00:0:0:175.13:11:175.13:0:0.00:0:0.00:50:2304.03:7555.46:2565.95:50:34:0:0.00:6:103.16:76 +6 26189702 gridss435f_9023b T TTTTTTCGGGTTTTTTGTTTTTTTCCCCTGTTTTAATTTATTGGCCCTTTATTTGCAAAATGAATACACTCGCACCCGGTTTAAAAAAATTAACCACCAAACCCCACCC. 1472.10 PON AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=6;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=596.29;BASRP=1;BASSR=25;BEID=asm435-14824,asm435-14825,asm435-14826,asm435-14831,asm435-14833,asm435-14839;BEIDH=-1,-1,-1,-1,-1,-1;BEIDL=0,0,0,0,0,0;BMQ=57.65;BMQN=40.00;BMQX=60.00;BQ=1512.79;BSC=40;BSCQ=858.12;BUM=2;BUMQ=58.39;BVF=42;CAS=0;CASQ=0.00;CQ=1384.86;EVENT=gridss435f_9023;IC=0;IQ=0.00;LOCAL_LINKED_BY=.;PURPLE_AF=0.175;PURPLE_CN=3.87;PURPLE_CN_CHANGE=0.00;PURPLE_JCN=0.677;RAS=0;RASQ=0.00;REF=100;REFG=TTTTTTTTTTTGAGACGGGTT;REFPAIR=139;REMOTE_LINKED_BY=.;RP=0;RPQ=0.00;SB=1.0;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.174;VF=0 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:20.34:0:1:40.68:1:20.34:0:0.00:1:0.00:0:0.00:0.00:0.00:20:25:0:0.00:0:0.00:0 .:0.00:0:0:0:0.00:0:0.00:575.94:1:24:1472.10:39:837.77:2:58.39:41:0.00:0:0.00:0.00:0.00:80:114:0:0.00:0:0.00:0 +6 26194040 gridss207bb_1124h A [3:26431918[A 6695.99 PASS AS=1;ASC=1X1D77M;ASQ=4132.75;ASRP=187;ASSR=74;BA=0;BANRP=0;BANRPQ=0.00;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm435-14858,asm435-30703;BEIDH=455,0;BEIDL=378,752;BMQ=59.71;BMQN=52.00;BMQX=60.00;BQ=3384.41;BSC=54;BSCQ=961.65;BUM=83;BUMQ=2422.76;BVF=3;CAS=1;CASQ=1711.53;CIPOS=-1,1;CIRPOS=-1,1;CQ=6663.85;EVENT=gridss207bb_1124;HOMLEN=2;HOMSEQ=CA;IC=0;IHOMPOS=-1,1;IQ=0.00;LOCAL_LINKED_BY=asm435-14858/378;MATEID=gridss207bb_1124o;MQ=59.73;MQN=44.00;MQX=60.00;PURPLE_AF=0.450,0.300;PURPLE_CN=7.35,11.84;PURPLE_CN_CHANGE=3.48,3.85;PURPLE_JCN=3.43;RAS=0;RASQ=0.00;REF=160;REFG=AATATCCAGCAATCTTAGACA;REFPAIR=126;REMOTE_LINKED_BY=.;RP=53;RPQ=851.71;SB=0.325;SC=1X288M;SR=0;SRQ=0.00;SVTYPE=BND;TAF=0.449;VF=189 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:28.92:0:0.00:1:28.92:1:0.00:0:0.00:0.00:0.00:28:26:0:0.00:0:0.00:0 .:4132.75:187:74:0:0.00:0:0.00:0.00:0:0:3355.50:54:961.65:82:2393.84:2:1711.53:0:0.00:6695.99:0.00:132:100:53:851.71:0:0.00:189 +6 26194117 gridss435ff_626o G G]6:26194406] 4118.20 PASS AS=1;ASC=76M1X;ASQ=989.45;ASRP=57;ASSR=106;BA=0;BANRP=1;BANRPQ=16.07;BANSR=0;BANSRQ=0.00;BAQ=0.00;BASRP=0;BASSR=0;BEID=asm435-14858,asm435-14859;BEIDH=0,89;BEIDL=378,0;BMQ=59.94;BMQN=59.00;BMQX=60.00;BQ=291.72;BSC=14;BSCQ=233.34;BUM=2;BUMQ=58.39;BVF=0;CAS=0;CASQ=0.00;CQ=4118.20;EVENT=gridss435ff_626;IC=0;IHOMPOS=0,0;IQ=0.00;LOCAL_LINKED_BY=asm435-14858/378;MATEID=gridss435ff_626h;MQ=59.64;MQN=52.00;MQX=60.00;PURPLE_AF=0.250,0.310;PURPLE_CN=7.35,5.53;PURPLE_CN_CHANGE=1.82,1.72;PURPLE_JCN=1.78;RAS=1;RASQ=2324.43;REF=185;REFG=CAGATATCCAGCAACCATCCA;REFPAIR=147;REMOTE_LINKED_BY=.;RP=3;RPQ=48.21;SB=0.35;SC=79M1X;SR=40;SRQ=756.11;SVTYPE=BND;TAF=0.249;VF=93 GT:ASQ:ASRP:ASSR:BANRP:BANRPQ:BANSR:BANSRQ:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:0.00:0:0:0:0.00:0:0.00:0.00:0:0:0.00:0:0.00:0:0.00:0:0.00:0:0.00:0.00:0.00:23:29:0:0.00:0:0.00:0 .:989.45:57:106:1:16.07:0:0.00:0.00:0:0:291.72:14:233.34:2:58.39:0:0.00:0:0.00:4118.20:2324.43:162:118:3:48.21:40:756.11:93 diff --git a/test/fixtures/real/provenance/deepvariant_golden_vcf.json b/test/fixtures/real/provenance/deepvariant_golden_vcf.json new file mode 100644 index 0000000..392a37b --- /dev/null +++ b/test/fixtures/real/provenance/deepvariant_golden_vcf.json @@ -0,0 +1,12 @@ +{ + "id": "deepvariant_golden_vcf", + "source": "https://raw.githubusercontent.com/google/deepvariant/r1.9/deepvariant/testdata/golden.postprocess_single_site_output.vcf", + "obtain": "direct", + "command": "curl -sSL https://raw.githubusercontent.com/google/deepvariant/r1.9/deepvariant/testdata/golden.postprocess_single_site_output.vcf -o test/fixtures/real/deepvariant/golden.single_site.vcf", + "out": "test/fixtures/real/deepvariant/golden.single_site.vcf", + "sha256": "08116cb4d8cf16b6cd1726f2615afe071673d72b8a2966cea894a17222e31c44", + "license": "BSD-3-Clause", + "attribution": "Google DeepVariant (github.com/google/deepvariant), BSD-3-Clause", + "build": "unspecified", + "generated_at_utc": "2026-07-04T02:33:05.484Z" +} diff --git a/test/fixtures/real/provenance/deepvariant_gvcf.json b/test/fixtures/real/provenance/deepvariant_gvcf.json new file mode 100644 index 0000000..e86aef9 --- /dev/null +++ b/test/fixtures/real/provenance/deepvariant_gvcf.json @@ -0,0 +1,12 @@ +{ + "id": "deepvariant_gvcf", + "source": "https://raw.githubusercontent.com/google/deepvariant/r1.9/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf", + "obtain": "direct", + "command": "curl -sSL https://raw.githubusercontent.com/google/deepvariant/r1.9/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf -o test/fixtures/real/deepvariant/golden.gvcf.g.vcf", + "out": "test/fixtures/real/deepvariant/golden.gvcf.g.vcf", + "sha256": "67c82cd23234a00160ab4101800e8a116cb25a10424241809f3b6474e709a605", + "license": "BSD-3-Clause", + "attribution": "Google DeepVariant (github.com/google/deepvariant), BSD-3-Clause", + "build": "unspecified", + "generated_at_utc": "2026-07-04T02:33:05.992Z" +} diff --git a/test/fixtures/real/provenance/freebayes_tiny_vcf.json b/test/fixtures/real/provenance/freebayes_tiny_vcf.json new file mode 100644 index 0000000..f88eb1c --- /dev/null +++ b/test/fixtures/real/provenance/freebayes_tiny_vcf.json @@ -0,0 +1,12 @@ +{ + "id": "freebayes_tiny_vcf", + "source": "https://raw.githubusercontent.com/freebayes/freebayes/master/test/regression_baseline/tiny_chr22.vcf", + "obtain": "direct", + "command": "curl -sSL https://raw.githubusercontent.com/freebayes/freebayes/master/test/regression_baseline/tiny_chr22.vcf -o test/fixtures/real/freebayes/tiny_chr22.vcf", + "out": "test/fixtures/real/freebayes/tiny_chr22.vcf", + "sha256": "c6d2b95edff43847e4398edce253e1ced59933ffd8a66e104a389e7c4d9bac33", + "license": "MIT", + "attribution": "freebayes (github.com/freebayes/freebayes), MIT", + "build": "unspecified", + "generated_at_utc": "2026-07-04T02:33:06.365Z" +} diff --git a/test/fixtures/real/provenance/gencode_gff3_chr22.json b/test/fixtures/real/provenance/gencode_gff3_chr22.json new file mode 100644 index 0000000..5af7ecc --- /dev/null +++ b/test/fixtures/real/provenance/gencode_gff3_chr22.json @@ -0,0 +1,12 @@ +{ + "id": "gencode_gff3_chr22", + "source": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.basic.annotation.gff3.gz", + "obtain": "gunzip-grep-slice", + "command": "curl https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.basic.annotation.gff3.gz | gzip -dc | grep \"^chr22\t\" (kept 300)", + "out": "test/fixtures/real/gencode/gencode.v50.basic.chr22.gff3", + "sha256": "4e38f0bae0e01149c8e33b030163f9598a5bc2f562f3d7e7657bc288a13b9409", + "license": "GENCODE / EMBL-EBI open", + "attribution": "GENCODE release 50 (basic annotation)", + "build": "GRCh38.p14", + "generated_at_utc": "2026-07-04T02:35:43.680Z" +} diff --git a/test/fixtures/real/provenance/gencode_gtf_chr22.json b/test/fixtures/real/provenance/gencode_gtf_chr22.json new file mode 100644 index 0000000..54164f7 --- /dev/null +++ b/test/fixtures/real/provenance/gencode_gtf_chr22.json @@ -0,0 +1,12 @@ +{ + "id": "gencode_gtf_chr22", + "source": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.basic.annotation.gtf.gz", + "obtain": "gunzip-grep-slice", + "command": "curl https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.basic.annotation.gtf.gz | gzip -dc | grep \"^chr22\t\" (kept 300)", + "out": "test/fixtures/real/gencode/gencode.v50.basic.chr22.gtf", + "sha256": "d21046f8997483020d6c3664c6405ced3817c8ab29f1e594750427954cab9d99", + "license": "GENCODE / EMBL-EBI open", + "attribution": "GENCODE release 50 (basic annotation)", + "build": "GRCh38.p14", + "generated_at_utc": "2026-07-04T02:34:09.249Z" +} diff --git a/test/fixtures/real/provenance/giab_hg002_bed.json b/test/fixtures/real/provenance/giab_hg002_bed.json new file mode 100644 index 0000000..e6a88f3 --- /dev/null +++ b/test/fixtures/real/provenance/giab_hg002_bed.json @@ -0,0 +1,12 @@ +{ + "id": "giab_hg002_bed", + "source": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed", + "obtain": "grep-slice", + "command": "curl https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed | grep \"^chr20\t\" (kept 200)", + "out": "test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_regions.bed", + "sha256": "b98292fd5d663e761f55793556e17b741b92764dc83d71c21ddb318e237de8ef", + "license": "NIST GIAB public benchmark (consented for redistribution)", + "attribution": "NIST Genome in a Bottle, HG002 NISTv4.2.1 GRCh38 benchmark regions", + "build": "GRCh38", + "generated_at_utc": "2026-07-04T02:37:04.659Z" +} diff --git a/test/fixtures/real/provenance/giab_hg002_vcf.json b/test/fixtures/real/provenance/giab_hg002_vcf.json new file mode 100644 index 0000000..f1e3dd7 --- /dev/null +++ b/test/fixtures/real/provenance/giab_hg002_vcf.json @@ -0,0 +1,12 @@ +{ + "id": "giab_hg002_vcf", + "source": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz", + "obtain": "tabix", + "command": "tabix -h https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz chr20:10000000-10020000 | bgzip; tabix -p vcf", + "out": "test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz", + "sha256": "34bfa39b77a850254a14d24900e12a17a83759e8122319c5bfba008880f25a84", + "license": "NIST GIAB public benchmark (consented for redistribution)", + "attribution": "NIST Genome in a Bottle, HG002 NISTv4.2.1 GRCh38 benchmark", + "build": "GRCh38", + "generated_at_utc": "2026-07-04T02:33:09.833Z" +} diff --git a/test/fixtures/real/provenance/gridss_sv_vcf.json b/test/fixtures/real/provenance/gridss_sv_vcf.json new file mode 100644 index 0000000..cd1cc82 --- /dev/null +++ b/test/fixtures/real/provenance/gridss_sv_vcf.json @@ -0,0 +1,12 @@ +{ + "id": "gridss_sv_vcf", + "source": "https://raw.githubusercontent.com/PapenfussLab/gridss/master/example/COLO829v003T.purple.sv.vcf", + "obtain": "head", + "command": "curl https://raw.githubusercontent.com/PapenfussLab/gridss/master/example/COLO829v003T.purple.sv.vcf | head (kept 60 data rows)", + "out": "test/fixtures/real/gridss/COLO829v003T.sv.slice.vcf", + "sha256": "2104bd429a22deea8213529abdca4e60bbfcaa8988f8705492f130c5b37b8dc9", + "license": "GPL-3.0", + "attribution": "GRIDSS (github.com/PapenfussLab/gridss), GPL-3.0", + "build": "hg19-like (example)", + "generated_at_utc": "2026-07-04T02:33:06.577Z" +} diff --git a/test/fixtures/real/provenance/kg_1000g_chr22_vcf.json b/test/fixtures/real/provenance/kg_1000g_chr22_vcf.json new file mode 100644 index 0000000..3b930b1 --- /dev/null +++ b/test/fixtures/real/provenance/kg_1000g_chr22_vcf.json @@ -0,0 +1,12 @@ +{ + "id": "kg_1000g_chr22_vcf", + "source": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz", + "obtain": "tabix", + "command": "tabix -h https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz 22:16050000-16070000 | bgzip; tabix -p vcf", + "out": "test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz", + "sha256": "f9118c92cc5499765e5cb6b9dd09e77416dadb353529f4dfe915f5f38dd4c07f", + "license": "IGSR / 1000 Genomes open data", + "attribution": "IGSR / 1000 Genomes Project, phase 3 (release 20130502)", + "build": "GRCh37", + "generated_at_utc": "2026-07-04T02:33:17.300Z" +} diff --git a/test/fixtures/real/provenance/ucsc_hg38_chrom_sizes.json b/test/fixtures/real/provenance/ucsc_hg38_chrom_sizes.json new file mode 100644 index 0000000..8ab7d81 --- /dev/null +++ b/test/fixtures/real/provenance/ucsc_hg38_chrom_sizes.json @@ -0,0 +1,12 @@ +{ + "id": "ucsc_hg38_chrom_sizes", + "source": "http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes", + "obtain": "head", + "command": "curl http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes | head (kept 30 data rows)", + "out": "test/fixtures/real/ucsc/hg38.chrom.sizes", + "sha256": "e04c1d358deda859aaac215782a00eae322756fe0766607292039685c6b9a927", + "license": "UCSC Genome Browser open download", + "attribution": "UCSC Genome Browser, hg38.chrom.sizes", + "build": "hg38", + "generated_at_utc": "2026-07-04T02:35:43.883Z" +} diff --git a/test/fixtures/real/provenance/ucsc_psl_example.json b/test/fixtures/real/provenance/ucsc_psl_example.json new file mode 100644 index 0000000..28f1f28 --- /dev/null +++ b/test/fixtures/real/provenance/ucsc_psl_example.json @@ -0,0 +1,12 @@ +{ + "id": "ucsc_psl_example", + "source": "https://genome.ucsc.edu/goldenpath/help/examples/bigPsl.psl", + "obtain": "direct", + "command": "curl -sSL https://genome.ucsc.edu/goldenpath/help/examples/bigPsl.psl -o test/fixtures/real/ucsc/bigPsl.psl", + "out": "test/fixtures/real/ucsc/bigPsl.psl", + "sha256": "c3c335bec5fbd99f26411982fea86a3847d2aa2ff0430d14955f80407c4c7120", + "license": "UCSC Genome Browser open download", + "attribution": "UCSC Genome Browser, bigPsl.psl example", + "build": "hg38", + "generated_at_utc": "2026-07-04T02:35:44.085Z" +} diff --git a/test/fixtures/real/sources.json b/test/fixtures/real/sources.json new file mode 100644 index 0000000..7eda839 --- /dev/null +++ b/test/fixtures/real/sources.json @@ -0,0 +1,173 @@ +{ + "$comment": "Manifest of license-vetted real-world fixtures. Source of truth for scripts/fetch-real-fixtures.ts (dev-only, network) and test/unit/real-fixtures.test.ts (offline). Committed fixtures are generated artifacts; sha256 is pinned by the fetch script. See ATTRIBUTION.md.", + "version": 1, + "root": "test/fixtures/real", + "entries": [ + { + "id": "deepvariant_golden_vcf", + "languageId": "omics-vcf", + "license": "BSD-3-Clause", + "attribution": "Google DeepVariant (github.com/google/deepvariant), BSD-3-Clause", + "build": "unspecified", + "obtain": "direct", + "source": "https://raw.githubusercontent.com/google/deepvariant/r1.9/deepvariant/testdata/golden.postprocess_single_site_output.vcf", + "out": "test/fixtures/real/deepvariant/golden.single_site.vcf", + "sha256": "08116cb4d8cf16b6cd1726f2615afe071673d72b8a2966cea894a17222e31c44", + "expect": { + "minRows": 1 + } + }, + { + "id": "deepvariant_gvcf", + "languageId": "omics-vcf", + "license": "BSD-3-Clause", + "attribution": "Google DeepVariant (github.com/google/deepvariant), BSD-3-Clause", + "build": "unspecified", + "obtain": "direct", + "source": "https://raw.githubusercontent.com/google/deepvariant/r1.9/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf", + "out": "test/fixtures/real/deepvariant/golden.gvcf.g.vcf", + "sha256": "67c82cd23234a00160ab4101800e8a116cb25a10424241809f3b6474e709a605", + "expect": { + "minRows": 1 + } + }, + { + "id": "freebayes_tiny_vcf", + "languageId": "omics-vcf", + "license": "MIT", + "attribution": "freebayes (github.com/freebayes/freebayes), MIT", + "build": "unspecified", + "obtain": "direct", + "source": "https://raw.githubusercontent.com/freebayes/freebayes/master/test/regression_baseline/tiny_chr22.vcf", + "out": "test/fixtures/real/freebayes/tiny_chr22.vcf", + "sha256": "c6d2b95edff43847e4398edce253e1ced59933ffd8a66e104a389e7c4d9bac33", + "expect": { + "minRows": 3 + } + }, + { + "id": "gridss_sv_vcf", + "languageId": "omics-vcf", + "license": "GPL-3.0", + "attribution": "GRIDSS (github.com/PapenfussLab/gridss), GPL-3.0", + "build": "hg19-like (example)", + "obtain": "head", + "headDataRows": 60, + "source": "https://raw.githubusercontent.com/PapenfussLab/gridss/master/example/COLO829v003T.purple.sv.vcf", + "out": "test/fixtures/real/gridss/COLO829v003T.sv.slice.vcf", + "sha256": "2104bd429a22deea8213529abdca4e60bbfcaa8988f8705492f130c5b37b8dc9", + "expect": { + "minRows": 5 + } + }, + { + "id": "giab_hg002_vcf", + "languageId": "omics-vcf", + "license": "NIST GIAB public benchmark (consented for redistribution)", + "attribution": "NIST Genome in a Bottle, HG002 NISTv4.2.1 GRCh38 benchmark", + "build": "GRCh38", + "obtain": "tabix", + "region": "chr20:10000000-10020000", + "source": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz", + "out": "test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_10.0-10.02Mb.vcf.gz", + "sha256": "34bfa39b77a850254a14d24900e12a17a83759e8122319c5bfba008880f25a84", + "expect": { + "minRows": 20, + "regionQuery": "chr20:10000000-10020000" + } + }, + { + "id": "giab_hg002_bed", + "languageId": "omics-bed", + "license": "NIST GIAB public benchmark (consented for redistribution)", + "attribution": "NIST Genome in a Bottle, HG002 NISTv4.2.1 GRCh38 benchmark regions", + "build": "GRCh38", + "obtain": "grep-slice", + "sliceChromPrefix": "chr20\t", + "sliceRows": 200, + "source": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed", + "out": "test/fixtures/real/giab/HG002_GRCh38_v4.2.1_chr20_regions.bed", + "sha256": "b98292fd5d663e761f55793556e17b741b92764dc83d71c21ddb318e237de8ef", + "expect": { + "minRows": 20 + } + }, + { + "id": "kg_1000g_chr22_vcf", + "languageId": "omics-vcf", + "license": "IGSR / 1000 Genomes open data", + "attribution": "IGSR / 1000 Genomes Project, phase 3 (release 20130502)", + "build": "GRCh37", + "obtain": "tabix", + "region": "22:16050000-16070000", + "source": "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz", + "out": "test/fixtures/real/1000g/1000g_phase3_chr22_16.05-16.07Mb.vcf.gz", + "sha256": "f9118c92cc5499765e5cb6b9dd09e77416dadb353529f4dfe915f5f38dd4c07f", + "expect": { + "minRows": 20, + "regionQuery": "22:16050000-16070000" + } + }, + { + "id": "gencode_gtf_chr22", + "languageId": "omics-gtf", + "license": "GENCODE / EMBL-EBI open", + "attribution": "GENCODE release 50 (basic annotation)", + "build": "GRCh38.p14", + "obtain": "gunzip-grep-slice", + "sliceChromPrefix": "chr22\t", + "sliceRows": 300, + "source": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.basic.annotation.gtf.gz", + "out": "test/fixtures/real/gencode/gencode.v50.basic.chr22.gtf", + "sha256": "d21046f8997483020d6c3664c6405ced3817c8ab29f1e594750427954cab9d99", + "expect": { + "minRows": 20 + } + }, + { + "id": "gencode_gff3_chr22", + "languageId": "omics-gff3", + "license": "GENCODE / EMBL-EBI open", + "attribution": "GENCODE release 50 (basic annotation)", + "build": "GRCh38.p14", + "obtain": "gunzip-grep-slice", + "sliceChromPrefix": "chr22\t", + "sliceRows": 300, + "source": "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_50/gencode.v50.basic.annotation.gff3.gz", + "out": "test/fixtures/real/gencode/gencode.v50.basic.chr22.gff3", + "sha256": "4e38f0bae0e01149c8e33b030163f9598a5bc2f562f3d7e7657bc288a13b9409", + "expect": { + "minRows": 20 + } + }, + { + "id": "ucsc_hg38_chrom_sizes", + "languageId": "omics-chrom-sizes", + "license": "UCSC Genome Browser open download", + "attribution": "UCSC Genome Browser, hg38.chrom.sizes", + "build": "hg38", + "obtain": "head", + "headDataRows": 30, + "source": "http://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes", + "out": "test/fixtures/real/ucsc/hg38.chrom.sizes", + "sha256": "e04c1d358deda859aaac215782a00eae322756fe0766607292039685c6b9a927", + "expect": { + "minRows": 20 + } + }, + { + "id": "ucsc_psl_example", + "languageId": "omics-psl", + "license": "UCSC Genome Browser open download", + "attribution": "UCSC Genome Browser, bigPsl.psl example", + "build": "hg38", + "obtain": "direct", + "source": "https://genome.ucsc.edu/goldenpath/help/examples/bigPsl.psl", + "out": "test/fixtures/real/ucsc/bigPsl.psl", + "sha256": "c3c335bec5fbd99f26411982fea86a3847d2aa2ff0430d14955f80407c4c7120", + "expect": { + "minRows": 1 + } + } + ] +} diff --git a/test/fixtures/real/ucsc/bigPsl.psl b/test/fixtures/real/ucsc/bigPsl.psl new file mode 100644 index 0000000..fb40130 --- /dev/null +++ b/test/fixtures/real/ucsc/bigPsl.psl @@ -0,0 +1,100 @@ +1579 25 0 0 0 0 2 884 + mAM992877 1604 0 1604 chr1 248956422 11873 14361 3 354,109,1141, 0,354,463, 11873,12612,13220, +1419 21 0 0 0 0 2 1048 + mAM992881 1440 0 1440 chr1 248956422 11873 14361 3 354,127,959, 0,354,481, 11873,12594,13402, +1533 12 0 0 0 0 4 944 + mAM992878 1545 0 1545 chr1 248956422 11873 14362 5 354,52,436,299,404, 0,354,406,842,1141, 11873,12645,13220,13658,13958, +1578 27 0 0 0 0 2 884 + mAM992879 1605 0 1605 chr1 248956422 11873 14362 3 354,109,1142, 0,354,463, 11873,12612,13220, +1652 0 0 0 0 0 2 884 + mAM992871 1652 0 1652 chr1 248956422 11873 14409 3 354,109,1189, 0,354,463, 11873,12612,13220, +1650 2 0 0 0 0 2 884 + mAM992872 1652 0 1652 chr1 248956422 11873 14409 3 354,109,1189, 0,354,463, 11873,12612,13220, +1648 4 0 0 0 0 2 884 + mAM992875 1652 0 1652 chr1 248956422 11873 14409 3 354,109,1189, 0,354,463, 11873,12612,13220, +1485 3 0 0 0 0 2 1048 + mAM992880 1488 0 1488 chr1 248956422 11873 14409 3 354,127,1007, 0,354,481, 11873,12594,13402, +1631 8 0 0 0 0 4 897 + mBC032353 1673 0 1639 chr1 248956422 11873 14409 5 354,109,737,300,139, 0,354,463,1200,1500, 11873,12612,13220,13958,14270, +1241 7 0 0 0 0 3 502 + mAM992873 1248 0 1248 chr1 248956422 12612 14362 4 109,436,299,404, 0,109,545,844, 12612,13220,13658,13958, +23 0 0 0 0 0 0 0 + mJD190877 23 0 23 chr1 248956422 12993 13016 1 23, 0, 12993, +23 0 0 0 0 0 0 0 + mJD167845 23 0 23 chr1 248956422 13001 13024 1 23, 0, 13001, +21 0 0 0 0 0 0 0 + mJD469098 23 2 23 chr1 248956422 13003 13024 1 21, 2, 13003, +20 0 0 0 0 0 0 0 + mJD485136 20 0 20 chr1 248956422 13087 13107 1 20, 0, 13087, +969 5 0 0 0 0 2 13 + mBC070227 1004 0 974 chr1 248956422 13420 14407 3 537,301,136, 0,537,838, 13420,13958,14271, +24 0 0 0 0 0 0 0 + mJD282506 24 0 24 chr1 248956422 13721 13745 1 24, 0, 13721, +32 0 0 0 0 0 0 0 + mJD192765 32 0 32 chr1 248956422 13877 13909 1 32, 0, 13877, +32 0 0 0 0 0 0 0 + mJD191631 32 0 32 chr1 248956422 13932 13964 1 32, 0, 13932, +32 0 0 0 0 0 0 0 + mJD135207 32 0 32 chr1 248956422 13939 13971 1 32, 0, 13939, +21 0 0 0 0 0 0 0 + mJD157229 21 0 21 chr1 248956422 14002 14023 1 21, 0, 14002, +24 0 0 0 0 0 0 0 + mJD199172 24 0 24 chr1 248956422 14241 14265 1 24, 0, 14241, +32 0 0 0 0 0 0 0 + mJD422311 32 0 32 chr1 248956422 14246 14278 1 32, 0, 14246, +32 0 0 0 0 0 0 0 + mJD108953 32 0 32 chr1 248956422 14322 14354 1 32, 0, 14322, +29 0 0 0 0 0 0 0 + mJD227419 32 1 30 chr1 248956422 14378 14407 1 29, 1, 14378, +2132 7 0 0 2 7 10 2693 - mBC063555 2219 0 2146 chr1 248956422 14404 19236 12 51,374,69,110,41,159,198,510,147,102,54,324, 73,129,503,572,684,725,884,1082,1592,1739,1841,1895, 14404,14455,14969,15795,15906,16606,16857,17232,17914,18267,18500,18912, +2543 19 0 0 1 1 10 2754 - mBC063893 2580 0 2563 chr1 248956422 14404 19720 12 107,316,69,108,44,159,198,126,381,147,99,808, 17,124,440,509,618,662,821,1019,1145,1526,1673,1772, 14404,14513,14969,15795,15903,16606,16857,17232,17361,17914,18267,18912, +2364 8 0 0 2 7 10 2987 - mBC053987 2406 0 2379 chr1 248956422 14404 19763 12 51,374,69,110,41,159,198,136,137,147,99,851, 27,83,457,526,638,679,838,1036,1172,1309,1456,1555, 14404,14455,14969,15795,15906,16606,16857,17232,17605,17914,18267,18912, +3455 40 0 0 2 3 10 182100 - mAL137714 3536 0 3498 chr1 248956422 14404 199999 13 107,316,281,299,559,661,198,512,47,99,99,154,163, 38,145,461,742,1043,1602,2263,2461,2973,3021,3120,3219,3373, 14404,14513,14969,185765,186064,186626,187379,187754,188438,188485,188790,195262,199836, +1663 29 0 0 3 16 10 8795 - mBC048328 1748 12 1720 chr1 248956422 14404 24891 13 51,374,69,110,41,116,46,199,136,137,147,112,154, 28,84,458,527,639,680,805,851,1050,1186,1323,1470,1582, 14404,14455,14969,15795,15906,16606,16722,16856,17232,17605,17914,18267,24737, +1563 6 0 0 2 7 7 13373 - mBC063470 1642 0 1576 chr1 248956422 14404 29346 9 51,374,110,41,159,198,456,154,26, 66,122,496,608,649,808,1006,1462,1616, 14404,14455,15795,15906,16606,16857,17605,24737,29320, +1576 19 0 0 1 1 11 13810 - mBX537637 1614 1 1597 chr1 248956422 14404 29809 13 91,12,34,108,44,159,198,136,137,147,99,154,276, 17,108,120,154,263,307,466,664,800,937,1084,1183,1337, 14404,14559,15004,15795,15903,16606,16857,17232,17605,17914,18267,24737,29533, +4213 21 0 0 1 2 2 93 - mAK024481 4236 0 4236 chr1 248956422 14406 18733 3 1499,859,1876, 0,1501,2360, 14406,15906,16857, +1931 21 0 0 2 2 13 183503 - mAK057951 1954 0 1954 chr1 248956422 14406 199861 16 423,69,108,44,162,199,136,140,25,99,156,14,99,99,154,25, 0,423,492,601,645,807,1006,1142,1282,1307,1406,1562,1577,1676,1775,1929, 14406,14969,15795,15903,16606,16856,17232,17605,18036,18267,24737,188471,188485,188790,195262,199836, +3135 19 0 0 2 7 7 11784 - mAK092583 3161 0 3161 chr1 248956422 14406 29344 9 49,1450,859,198,136,137,147,154,24, 0,54,1506,2365,2563,2699,2836,2983,3137, 14406,14455,15906,16857,17232,17605,17914,24737,29320, +3135 19 0 0 2 7 7 11784 - mAX747611 3161 0 3161 chr1 248956422 14406 29344 9 49,1450,859,198,136,137,147,154,24, 0,54,1506,2365,2563,2699,2836,2983,3137, 14406,14455,15906,16857,17232,17605,17914,24737,29320, +2334 13 0 0 2 7 12 13247 - mAK056232 2354 0 2354 chr1 248956422 14406 30000 14 49,374,69,110,41,162,199,136,137,147,99,154,582,88, 0,54,428,497,609,650,812,1011,1147,1284,1431,1530,1684,2266, 14406,14455,14969,15795,15906,16606,16856,17232,17605,17914,18267,24737,29320,29912, +2491 6 0 0 2 7 8 2204 - mBC094698 2535 0 2504 chr1 248956422 14407 19108 10 48,374,69,110,41,159,198,510,147,841, 31,84,458,527,639,680,839,1037,1547,1694, 14407,14455,14969,15795,15906,16606,16857,17232,17914,18267, +2295 34 0 0 2 7 12 2980 - mBC041177 2401 0 2336 chr1 248956422 14407 19716 14 48,374,69,110,41,116,37,199,136,137,147,112,278,525, 65,118,492,561,673,714,830,867,1066,1202,1339,1486,1598,1876, 14407,14455,14969,15795,15906,16606,16731,16856,17232,17605,17914,18267,18912,19191, +2339 34 0 0 2 7 11 2979 - mAY217347 2447 2 2382 chr1 248956422 14407 19759 13 48,374,69,110,41,116,37,199,136,137,147,112,847, 65,118,492,561,673,714,830,867,1066,1202,1339,1486,1598, 14407,14455,14969,15795,15906,16606,16731,16856,17232,17605,17914,18267,18912, +32 0 0 0 0 0 0 0 - mJD043865 32 0 32 chr1 248956422 14423 14455 1 32, 0, 14423, +32 0 0 0 0 0 0 0 - mJD464022 32 0 32 chr1 248956422 14453 14485 1 32, 0, 14453, +30 0 0 0 0 0 0 0 - mJD464023 32 0 30 chr1 248956422 14455 14485 1 30, 2, 14455, +32 0 0 0 0 0 0 0 - mJD426250 32 0 32 chr1 248956422 14496 14528 1 32, 0, 14496, +32 0 0 0 0 0 0 0 - mJD319762 32 0 32 chr1 248956422 14537 14569 1 32, 0, 14537, +32 0 0 0 0 0 0 0 - mJD439184 32 0 32 chr1 248956422 14538 14570 1 32, 0, 14538, +1636 28 0 0 2 11 11 13727 - mAK289708 1678 3 1678 chr1 248956422 14570 29961 13 259,69,110,41,116,46,199,136,137,147,112,154,138, 0,259,328,440,481,606,652,851,987,1124,1271,1383,1537, 14570,14969,15795,15906,16606,16722,16856,17232,17605,17914,18267,24737,29823, +28 0 0 0 0 0 0 0 + mDQ588205 28 0 28 chr1 248956422 14629 14657 1 28, 0, 14629, +24 0 0 0 0 0 0 0 + mJD033185 24 0 24 chr1 248956422 14643 14667 1 24, 0, 14643, +24 0 0 0 0 0 0 0 - mJD386972 24 0 24 chr1 248956422 14643 14667 1 24, 0, 14643, +32 0 0 0 0 0 0 0 - mJD469492 32 0 32 chr1 248956422 14673 14705 1 32, 0, 14673, +32 0 0 0 0 0 1 3 - mJD371043 32 0 32 chr1 248956422 14702 14737 2 15,17, 0,15, 14702,14720, +32 0 0 0 0 0 1 3 - mJD186991 32 0 32 chr1 248956422 14703 14738 2 14,18, 0,14, 14703,14720, +21 0 0 0 0 0 0 0 - mJD178321 21 0 21 chr1 248956422 14704 14725 1 21, 0, 14704, +32 0 0 0 0 0 0 0 - mJD371044 32 0 32 chr1 248956422 14705 14737 1 32, 0, 14705, +32 0 0 0 0 0 0 0 - mJD492409 32 0 32 chr1 248956422 14739 14771 1 32, 0, 14739, +24 0 0 0 0 0 0 0 - mJD248147 24 0 24 chr1 248956422 14746 14770 1 24, 0, 14746, +32 0 0 0 0 0 0 0 - mJD044295 32 0 32 chr1 248956422 14785 14817 1 32, 0, 14785, +32 0 0 0 0 0 0 0 - mJD433165 32 0 32 chr1 248956422 14810 14842 1 32, 0, 14810, +32 0 0 0 0 0 0 0 - mJD055458 32 0 32 chr1 248956422 14823 14855 1 32, 0, 14823, +25 0 0 0 0 0 0 0 - mJD131561 25 0 25 chr1 248956422 14828 14853 1 25, 0, 14828, +20 0 0 0 0 0 0 0 - mJD129847 20 0 20 chr1 248956422 14936 14956 1 20, 0, 14936, +21 0 0 0 0 0 0 0 - mJD219312 21 0 21 chr1 248956422 14950 14971 1 21, 0, 14950, +32 0 0 0 0 0 0 0 - mJD546847 32 0 32 chr1 248956422 15086 15118 1 32, 0, 15086, +32 0 0 0 0 0 0 0 - mJD218460 32 0 32 chr1 248956422 15097 15129 1 32, 0, 15097, +531 5 0 0 1 1 0 0 + mKJ806766 562 9 546 chr1 248956422 15118 15654 2 4,532, 9,14, 15118,15122, +32 0 0 0 0 0 0 0 - mJD131237 32 0 32 chr1 248956422 15187 15219 1 32, 0, 15187, +32 0 0 0 0 0 0 0 - mJD128091 32 0 32 chr1 248956422 15209 15241 1 32, 0, 15209, +31 0 0 0 0 0 0 0 - mJD422546 31 0 31 chr1 248956422 15274 15305 1 31, 0, 15274, +32 0 0 0 0 0 0 0 - mJD153435 32 0 32 chr1 248956422 15292 15324 1 32, 0, 15292, +32 0 0 0 0 0 0 0 - mJD367640 32 0 32 chr1 248956422 15461 15493 1 32, 0, 15461, +32 0 0 0 0 0 0 0 - mJD487131 32 0 32 chr1 248956422 15468 15500 1 32, 0, 15468, +32 0 0 0 0 0 0 0 - mJD493181 32 0 32 chr1 248956422 15480 15512 1 32, 0, 15480, +32 0 0 0 0 0 0 0 - mJD205712 32 0 32 chr1 248956422 15558 15590 1 32, 0, 15558, +32 0 0 0 0 0 0 0 - mJD425846 32 0 32 chr1 248956422 15584 15616 1 32, 0, 15584, +31 0 0 0 0 0 0 0 - mJD219639 32 1 32 chr1 248956422 15603 15634 1 31, 0, 15603, +32 0 0 0 0 0 0 0 - mJD078677 32 0 32 chr1 248956422 15603 15635 1 32, 0, 15603, +21 0 0 0 0 0 0 0 - mJD078676 21 0 21 chr1 248956422 15614 15635 1 21, 0, 15614, +32 0 0 0 0 0 0 0 - mJD253503 32 0 32 chr1 248956422 15643 15675 1 32, 0, 15643, +31 0 0 0 0 0 0 0 - mJD253504 32 0 31 chr1 248956422 15644 15675 1 31, 1, 15644, +23 0 0 0 0 0 0 0 - mJD159284 23 0 23 chr1 248956422 15664 15687 1 23, 0, 15664, +32 0 0 0 0 0 0 0 - mJD115871 32 0 32 chr1 248956422 15675 15707 1 32, 0, 15675, +32 0 0 0 0 0 0 0 - mJD456634 32 0 32 chr1 248956422 15677 15709 1 32, 0, 15677, +31 0 0 0 0 0 0 0 - mJD487879 32 1 32 chr1 248956422 15741 15772 1 31, 0, 15741, +32 0 0 0 0 0 0 0 - mJD080014 32 0 32 chr1 248956422 15741 15773 1 32, 0, 15741, +32 0 0 0 0 0 0 0 - mJD336830 32 0 32 chr1 248956422 15760 15792 1 32, 0, 15760, +32 0 0 0 0 0 0 0 - mJD444008 32 0 32 chr1 248956422 15761 15793 1 32, 0, 15761, +24 0 0 0 0 0 0 0 - mJD460507 24 0 24 chr1 248956422 15812 15836 1 24, 0, 15812, +1139 13 0 0 1 1 7 12337 - mAK308574 1153 0 1153 chr1 248956422 15870 29359 9 33,124,159,198,132,221,147,99,39, 0,34,158,317,515,647,868,1015,1114, 15870,15903,16606,16857,17232,17521,17914,18267,29320, +30 0 0 0 0 0 0 0 - mJD389037 32 0 30 chr1 248956422 15906 15936 1 30, 2, 15906, +32 0 0 0 0 0 0 0 - mJD521711 32 0 32 chr1 248956422 15947 15979 1 32, 0, 15947, +32 0 0 0 0 0 0 0 - mJD383617 32 0 32 chr1 248956422 15972 16004 1 32, 0, 15972, +32 0 0 0 0 0 0 0 - mJD491045 32 0 32 chr1 248956422 15982 16014 1 32, 0, 15982, +32 0 0 0 0 0 0 0 - mJD318660 32 0 32 chr1 248956422 15985 16017 1 32, 0, 15985, +32 0 0 0 0 0 0 0 - mJD341280 32 0 32 chr1 248956422 16118 16150 1 32, 0, 16118, +32 0 0 0 0 0 0 0 - mJD220623 32 0 32 chr1 248956422 16157 16189 1 32, 0, 16157, +32 0 0 0 0 0 0 0 - mJD465423 32 0 32 chr1 248956422 16165 16197 1 32, 0, 16165, +32 0 0 0 0 0 0 0 - mJD515432 32 0 32 chr1 248956422 16176 16208 1 32, 0, 16176, +32 0 0 0 0 0 0 0 - mJD542452 32 0 32 chr1 248956422 16184 16216 1 32, 0, 16184, +29 0 0 0 0 0 0 0 - mJD507246 30 1 30 chr1 248956422 16201 16230 1 29, 0, 16201, +21 0 0 0 0 0 0 0 - mJD102852 21 0 21 chr1 248956422 16253 16274 1 21, 0, 16253, diff --git a/test/fixtures/real/ucsc/hg38.chrom.sizes b/test/fixtures/real/ucsc/hg38.chrom.sizes new file mode 100644 index 0000000..5d19182 --- /dev/null +++ b/test/fixtures/real/ucsc/hg38.chrom.sizes @@ -0,0 +1,30 @@ +chr1 248956422 +chr2 242193529 +chr3 198295559 +chr4 190214555 +chr5 181538259 +chr6 170805979 +chr7 159345973 +chrX 156040895 +chr8 145138636 +chr9 138394717 +chr11 135086622 +chr10 133797422 +chr12 133275309 +chr13 114364328 +chr14 107043718 +chr15 101991189 +chr16 90338345 +chr17 83257441 +chr18 80373285 +chr20 64444167 +chr19 58617616 +chrY 57227415 +chr22 50818468 +chr21 46709983 +chr15_KI270905v1_alt 5161414 +chr6_GL000256v2_alt 4929269 +chr6_GL000254v2_alt 4827813 +chr6_GL000251v2_alt 4795265 +chr6_GL000253v2_alt 4677643 +chr6_GL000250v2_alt 4672374 diff --git a/test/unit/real-fixtures.test.ts b/test/unit/real-fixtures.test.ts new file mode 100644 index 0000000..bea85e5 --- /dev/null +++ b/test/unit/real-fixtures.test.ts @@ -0,0 +1,132 @@ +// SPDX-License-Identifier: GPL-3.0-or-later +// +// Offline verification of the committed real-world fixtures. Never touches the +// network (that is scripts/fetch-real-fixtures.ts, run manually). For each +// manifest entry with a committed file, this asserts the packaging contract and +// that BioFmt's real validator processes the real file without crashing. + +import * as assert from 'assert'; +import * as fs from 'fs'; +import * as path from 'path'; +import * as crypto from 'crypto'; +import { unzip } from '@gmod/bgzf-filehandle'; +import { TabixIndexedFile } from '@gmod/tabix'; +import { getValidator } from '../../server/src/validators'; +import { defaultSettings, type ValidatorContext } from '../../server/src/validators/types'; + +const REPO_ROOT = path.resolve(__dirname, '..', '..'); +const MANIFEST = path.join(REPO_ROOT, 'test', 'fixtures', 'real', 'sources.json'); + +interface Entry { + id: string; + languageId: string; + out: string; + sha256: string; + expect: { minRows: number; regionQuery?: string }; +} + +const manifest: { entries: Entry[] } = JSON.parse(fs.readFileSync(MANIFEST, 'utf8')); + +async function readText(abs: string): Promise { + const buf = fs.readFileSync(abs); + if (abs.endsWith('.gz')) { + const out = await unzip(buf); + return Buffer.from(out).toString('utf8'); + } + return buf.toString('utf8'); +} + +function sha256(abs: string): string { + return crypto.createHash('sha256').update(fs.readFileSync(abs)).digest('hex'); +} + +function dataRows(text: string): number { + return text.split(/\r?\n/).filter((l) => l.length > 0 && !l.startsWith('#')).length; +} + +describe('real-world fixtures', () => { + // Guard against the committed set silently shrinking: a manifest entry that has + // a pinned sha256 was fetched and committed, so its file (and index, for + // indexed entries) must still be present. Removing a fixture therefore requires + // a visible edit to sources.json — it can't quietly vanish while tests stay + // green (the per-entry checks below skip absent files by design). + it('every pinned fixture (and its index) is committed', () => { + const missing: string[] = []; + for (const entry of manifest.entries) { + if (!entry.sha256) continue; // not yet fetched/pinned — allowed to be absent + const abs = path.join(REPO_ROOT, entry.out); + if (!fs.existsSync(abs)) missing.push(entry.out); + if (entry.expect.regionQuery && !fs.existsSync(`${abs}.tbi`)) { + missing.push(`${entry.out}.tbi`); + } + } + assert.deepStrictEqual( + missing, + [], + `pinned fixtures missing from the repo (clear their sha256 in sources.json to intentionally drop them): ${missing.join(', ')}` + ); + }); + + for (const entry of manifest.entries) { + const abs = path.join(REPO_ROOT, entry.out); + + describe(entry.id, () => { + if (!fs.existsSync(abs)) { + it('is fetched (run: npm run fetch:fixtures)', function () { + this.skip(); + }); + return; + } + + it('matches the pinned sha256', () => { + if (!entry.sha256) return; // not pinned yet + assert.strictEqual(sha256(abs), entry.sha256, `checksum drift in ${entry.out}`); + }); + + it('is a format BioFmt supports', () => { + assert.strictEqual( + typeof getValidator(entry.languageId), + 'function', + `no validator for ${entry.languageId}` + ); + }); + + it('validates without throwing (robustness)', async () => { + const text = await readText(abs); + const validator = getValidator(entry.languageId)!; + const lineCount = text.split(/\r?\n/).length; + const ctx: ValidatorContext = { + uri: `file://${abs}`, + lineCount, + headerEndLine: 0, + bufferLines: 5000, + visibleRanges: [{ startLine: 0, endLine: lineCount }], + }; + let diags: unknown; + assert.doesNotThrow(() => { + diags = validator(text, defaultSettings, ctx); + }); + assert.ok(Array.isArray(diags), 'validator did not return a diagnostics array'); + }); + + it(`has at least ${entry.expect.minRows} data rows`, async () => { + const text = await readText(abs); + const n = dataRows(text); + assert.ok(n >= entry.expect.minRows, `expected >= ${entry.expect.minRows} rows, got ${n}`); + }); + + if (entry.expect.regionQuery) { + it('answers an indexed region query via @gmod/tabix', async () => { + const tbi = `${abs}.tbi`; + assert.ok(fs.existsSync(tbi), `missing index: ${tbi}`); + const [chrom, range] = entry.expect.regionQuery!.split(':'); + const [start, end] = range.split('-').map((v) => Number(v)); + const t = new TabixIndexedFile({ path: abs, tbiPath: tbi }); + const lines: string[] = []; + await t.getLines(chrom, start, end, { lineCallback: (l: string) => lines.push(l) }); + assert.ok(lines.length > 0, 'region query returned no records'); + }); + } + }); + } +});