Why Does This The Sam Record Having A Mapping Quality Of 0

Question

[huskerjeff492]

* 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

Answer 1

[Biomonika (Noolean)]

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?

[huskerjeff492]

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)

[KCC]

From what I understand the XT and XA flags arise from different algorithms to the mapping quality being 0. I read this a while ago.

[Biomonika (Noolean)]

Sorry, it wasn't clear for me from the post.