* Let me start by saying I totally understand what mapping quality 0 means *** So please don't post link to those posts.
I have posted two paired ends. One set has a mapping quality of 0 the other has score of 22 and 23. I can not find anything in the mapping quality 0 set that would indicate why these reads have a mapping quality score of 0. Can some please point out what I am missing.
grep M00386:31:000000000-A4L4V:1:2105:8182:14608 *.sam
M00386:31:000000000-A4L4V:1:2105:8182:14608 83 chr6 32009796 0 151M = 32009757 -190 GCCGTGGTAGCCCTCCAAGTGGAGGCGGTAGTACCCCGCAGCCGAGTCTACGTGGAAGGAGTCGTACTGGGCGAACACAGCCTCGTCCCCAGCCCGCAGGTCCACGCGCATGGAGTAGTCACCTGCCTGTGTCAGGCTGTGCAGGGCCTCA ?GEFGGGFEGGGHGHHHHGHHGGGGGHHHHHE<GGGGGGGFGGHHHFGF=GGHHHHGHGGGFGHHFHGGGGGHHFGGHHGGGGEEAGGGGGGGGGHHHHHGGGGGGGGHHHHHHGHFGHHHGGHGHHHHGGGGGGGGGGFCFCDDDDCCCC RG:Z:Default XT:A:R NM:i:1SM:i:0 AM:i:0 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:34T116 XA:Z:chr6,-31977061,151M,1;
M00386:31:000000000-A4L4V:1:2105:8182:14608 163 chr6 32009757 0 151M = 32009796 190 CTCACCCTCCCAGCCTCACAGCCTCTGCTTACCTGCGGTGCCGTGGTAGCCCTCCAAGTGGAGGCGGTAGTACCCCGCAGCCGAGTCTACGTGGAAGGAGGCGTACTGGGCGAACACAGCCTCGTCCCCCGCCCGCAGGGCCCCGCGCCTG DDCCDFFCDCDFGGGGGGGGGGHHHHHHHHHHHGHHGGEFGHGGGGHHFGHHHHGGHHGHHFHGGGGEE?3@BFGH/E//EF>/<?2F44/BBE/BGG?C/<B?B@GHFH=@/C-@0G0.F0>A.<DGH.<@CG-:--<-.<-<9?@?-<B RG:Z:Default XT:A:R NM:i:6SM:i:0 AM:i:0 X0:i:2 X1:i:0 XM:i:6 XO:i:0 XG:i:0 MD:Z:73T26T28A9T2A5A2 XA:Z:chr6,+31977022,151M,6;
grep M00386:31:000000000-A4L4V:1:2113:5719:18716 *.sam
M00386:31:000000000-A4L4V:1:2113:5719:18716 83 chr6 32010039 23 151M = 32009881 -309 TGACCCAGCCAGAACTCTCCAGAGATGTTCCCAAAACCATGGGCATAGTCCTCCCAGTCCCTCCAGAAGTCTGTCTGTCCATCCATGCGGCGCTGGAACACCTGGGAAGCAAGTGGGGGCACCATCAGCCTCTGGCTCCCGGGGCAACAGA HHHGGGGHHHHHHHGHHHHHHHHHHHGHHGCHGHHGHHHHHHHHHHHHGGGHHHHHGGGGHHHHHHHHHHHHHHGHGHGHHHHGGGGGGGGHHHHHGHGFGHHHHHHHHHHHFCGGHHHHGHHHHHHGGGGGGGGGGGGCCFFFFFCCCCC RG:Z:Default XT:A:U NM:i:0SM:i:23 AM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:151 XA:Z:chr6,-31977304,151M,1;
M00386:31:000000000-A4L4V:1:2113:5719:18716 163 chr6 32009881 22 151M = 32010039 309 TCCCCAGCCCGCAGGTCCACGCGCATGGAGTAGTCACCTGCCTGTGTCAGGCTGTGCAGGGCCTCATTGCCTGGGGGTGGGATACGTGCCCTCATCAGGGTCCTGGTATCCACAGGGCCCCCATCCCCATCCGTAGTTCCCCAGTCCCTGT BBABBFBFABBBGGGGGGGGGGGGGGGHFHHHHHHHHHHGHHHHGHHHGHHHHHHEHGHHGGGGHHHHGFHHHHGGGEEGGHHHHEHHHHHGHHHHHHHGHHHHHHH3HFHHHGHGGGGGGFGHFHHEGHFHGFHGGHHHHHHGHHGHFF< RG:Z:Default XT:A:R NM:i:1SM:i:0 AM:i:0 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:107G43 XA:Z:chr6,+31977146,151M,1;
Thank you
In BWA, mapping quality of 0 indicates that mapping to multiple positions is possible.
See What does the zero mapping quality mean for the BWA mapper?
I completely understand what mapping quality 0 means, however if you look at my sam record it does not to my knowledge reflect multiple alignments The XA or XT field (I have looked at many records with multiple alignments so know what they typically look like)
Sorry, it wasn't clear for me from the post.
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