Why does BWA give different Mapping Quality to identical reads?

Question

[Asdp]

Hi Biostars,

Below are two paired-end reads in sam format. The forward of the first and the forward of the second have the same start position and the same sequence. The first paired-end read has a mapping quality of 0 and the second has a mapping quality of 9. Zero mapping quality indicates that the read maps to multiple locations. But, in this case, the sequences are the same.
Why do these reads have different Mapping Quality? Thanks for your help!

HWI-1KL149:88:C41FMACXX:4:2208:12488:52749      163     1       155581760       0       100M    =       155581788       128     TTTACTTGTGGCAGGGAAGCAGGTCGGCTGGAGGCTTTTGGCCAAGGGGAAAGTGTCCTAAAGGAACCCAAGTACCAGGAAGAGCTGGAGGACAGGCTGC       CB@CEHAEDFDCFFCCBCEEEECDE?DDFGDDBDDEDCDCDCD?DEDDDE?FF;2BIDIEEGDC<DBIIIGAC>I7AHHEGAGGJ"9>DBHFDJHGFACA    XA:Z:1,+155717340,100M,0;  MC:Z:100M       BD:Z:NNFNRQNPMMPOPPOKNMNOOPONPONOOPPOOPOOMEEOPOOPNOQLMPOEPQNNQPPONEPQPOOPLQOPQPPPQRQPOPPQRQRRQQRRSPTTPPQQ       MD:Z:100        PG:Z:MarkDuplicates     RG:Z:p26   BI:Z:IIGKRQONMLLLJID?HHLKEGIKNJJNMOLMNKGB?=ADFHHLKJD<<EECCCGHMMMQOJKJMNQOMPPQPQPMNPNOPQPPOLKDBDFINPQOHGIK       NM:i:0  MQ:i:0  AS:i:100        XS:i:100
HWI-1KL149:88:C41FMACXX:4:2208:12488:52749      83      1       155581788       0       100M    =       155581760       -128    TGCAGGCTTTTGGCCAAGGGGATAGTGTCCTAAAGGAACCCAAGTACCAGGAAGAGCTGGAGGACAGGCTGCATTTCTACGTGGAGGAATGTGACTACTT       ###EGGHE<9JK?EGIJHF>@="JGHGEEFEEEGEGEEEEHEFFEEDGFDFDFFFFFFDFFDFDGFDEFFDGEDDDFDDAEFDFFDFDGGGFHHGED>DA    XA:Z:1,-155717368,100M,2;  MC:Z:100M       BD:Z:NNNPQSRGGPRQQRQNPLLPQOOPNNQPQPNFNPPOOPMQPNPPPPQQPOOMNNOPQPONOOPMPOOPQPPPNDNOOOONMPONOONOQNNQRRRRQPNN       MD:Z:2G19A77    PG:Z:MarkDuplicates     RG:Z:p26   BI:Z:IIIHIOPNNPPNONPPONNORRQPPMKHCEKKNNNQOOIIFA@>>CFLMNQONNLPPONONNPOONMPPLOOMJMPPPLMQONNMMPOPPQOPOPQIJII       NM:i:2  MQ:i:0  AS:i:92 XS:i:92

HWI-1KL149:88:C41FMACXX:4:1215:3187:9272        99      1       155581760       9       100M    =       155581855       195     TTTACTTGTGGCAGGGAAGCAGGTCGGCTGGAGGCTTTTGGCCAAGGGGAAAGTGTCCTAAAGGAACCCAAGTACCAGGAAGAGCTGGAGGACAGGCTGC       CC@DFJHF6DEGF?DD9C>8B@CBE7@DDED?ADEEDDDCAECEDBAADDEF??;<>GHEGGCCBBCIJECA>?DIIC=C@IGIKK?=B:67AG8?AB<=    XA:Z:1,+155717340,100M,0;  MC:Z:100M       BD:Z:NNFNRROQONQPQQPLONOPPQPOPONOOPPOOPOOMEEOPOOPNOPLLPNEPQNNQPPONEPQPOOPLQOPQPPPQRQPOPPPQQRRQQRRSPTRPPQQ       MD:Z:100        PG:Z:MarkDuplicates     RG:Z:p24   BI:Z:IIGKRPOOOOMNLOMJNOPPMPNOPIHKKMLOPNNMOMMOMNMOOOMJKOOLMHC==>@HLKPNOOQNKIDEHKNNOPOPPQQQQNPNPQOPQPOJHGIK       NM:i:0  MQ:i:9  AS:i:100        XS:i:100
HWI-1KL149:88:C41FMACXX:4:1215:3187:9272        147     1       155581855       9       100M    =       155581760       -195    GCTGCATTTCTACGTGGAGGAATGTGACTACTTGCAGGTAGTGGCGTGGCAATGTGCACTCCAGGGTGGAAGCTCTTCTCATCCTGCTAACTATCTTTTG       FCBCGHHHHHCHEJJHIJJIICHGBDFGFDFGGGCDFFDEFFDE@AFBDFBDFFED?AFDDGEDDFADFDED=??ACD@FDC?EEEBE8=B7FA@ED?C@    XA:Z:1,-155717435,100M,1;  MC:Z:100M       BD:Z:QRQQTQGQRQQQPORQPPPOOQNNPQQPPQPOQQQPPPOPNQPOONQPQPOQMNPPMPOOPPOKOMPONMOPOOONNNOONNOPOONMNPONPPQGEONN       MD:Z:100        PG:Z:MarkDuplicates     RG:Z:p24   BI:Z:JJGKRQMMJHD?DMNMONORPPPPMOPQQPQOMQNLKLNOQNLJFIC@GEFAAGGMLJJHBC>=DJLLONMPPOOMLKGIKKGIAFINMNMOOPQNGIII       NM:i:0  MQ:i:9  AS:i:100        XS:i:98

[Brian Bushnell]

"...POOPOOMEEOPOOPNO..."

I'm guessing this is a fecal microbiome...?

[Ashutosh Pandey]

Seems you have been doing a lot of metagenomics lately :-)

[Ashutosh Pandey]

May be you pasted the wrong read. I can't see read with MAPQ of 9.

[Asdp]

Fixed. Thanks.

Answer 1

[matted]

The other reads in the pairs map to different locations (155581788 vs 155581855), and that affects the mapping quality since pairs are evaluated together in bwa (see e.g. http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores).