missunderstanding of -p and -N options

[mariabernard]

Hello,

I am playing with -p option to limit the number of secondary alignment to those that have the same alignment score:

minimap2 -ax map-ont GCF_002863925.1_EquCab3.0_genomic.mmi test.fastq > test_default.sam
minimap2 -p 1.0 -ax map-ont GCF_002863925.1_EquCab3.0_genomic.mmi test.fastq > test_p1.sam
minimap2 -p 0 -ax map-ont GCF_002863925.1_EquCab3.0_genomic.mmi test.fastq > test_p0.sam
minimap2 -p 0 -N5 -ax map-ont  GCF_002863925.1_EquCab3.0_genomic.mmi test.fastq > test_p0_N5.sam

• Default setting (-p 0.8) and -p1 give the same results

f3bdc742-6667-4b62-85ea-8edc42d1218c	0	NW_019643253.1	154	0	121M1S	*	0	0	GCT...CGA NQN...KFD	NM:i:0	ms:i:242	AS:i:242	nn:i:0	tp:A:P	cm:i:20	s1:i:110	s2:i:110	de:f:0	rl:i:0
f3bdc742-6667-4b62-85ea-8edc42d1218c	256	NW_019643246.1	2461	0	121M1S	*	0	0	*	*	NM:i:0ms:i:242	AS:i:242	nn:i:0	tp:A:S	cm:i:20	s1:i:110	de:f:0	rl:i:0
f3bdc742-6667-4b62-85ea-8edc42d1218c	272	NW_019643250.1	3054	0	1S121M	*	0	0	*	*	NM:i:0ms:i:242	AS:i:242	nn:i:0	tp:A:S	cm:i:20	s1:i:110	de:f:0	rl:i:0
f3bdc742-6667-4b62-85ea-8edc42d1218c	272	NW_019645690.1	3623	0	1S121M	*	0	0	*	*	NM:i:0ms:i:242	AS:i:242	nn:i:0	tp:A:S	cm:i:20	s1:i:110	de:f:0	rl:i:0
f3bdc742-6667-4b62-85ea-8edc42d1218c	272	NW_019643245.1	6918	0	1S121M	*	0	0	*	*	NM:i:0ms:i:242	AS:i:242	nn:i:0	tp:A:S	cm:i:20	s1:i:110	de:f:0	rl:i:0
f3bdc742-6667-4b62-85ea-8edc42d1218c	256	NC_009174.3	1	0	24S55M1D42M1S	*	0	0	*	*	NM:i:1	ms:i:188	AS:i:188	nn:i:0	tp:A:S	cm:i:14	s1:i:85	de:f:0.0102	rl:i:0

This give me 6 alignements 1 primary and 5 secondary. 4 of them seems to be equivalent same ciga, same AS.
But the last one as AS=188 and chain score s2=85, compare to the primary alignment AS=242 and s1=110.

even with -p 0.8 (default value), why this last alignment is returned ? secondary-to-primary score give ~77% (on AS or on s1).

• p0 and p0 & N5 give ce same results
  We could expect that as the default value of N is 5, but in that cas minimap2 returned à 6th alignment which indeed is woorst in terms of chain score, s1=83 compare to s1 =110 (or 85).

f3bdc742-6667-4b62-85ea-8edc42d1218c	272	NC_009146.3	X	0	1S103M1I9M8S	*	0	0	*	*	NM:i:3	ms:i:206	AS:i:206	nn:i:0	tp:A:S	cm:i:14	s1:i:83	de:f:0.0265	rl:i:0

So I am not sure to understand how -p and -N work?
Is there any possibility to return only "equivalent best alignments" ?

Kind regards

Maria