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I have a question related to the output of FlagStat. I used BWA mem with version 0.7.4 to align the reads and following is the output of FlagStat
1290814928 in total
0 QC failure
1269372151 mapped (98.34%)
1290814928 paired in sequencing
0 properly paired (0.00%)
1264066894 with itself and mate mapped
5305257 singletons (0.41%)
54566084 with mate mapped to a different chr
13502927 with mate mapped to a different chr (mapQ>=5)
In output,1290814928 paired in sequencing, but 0% are properly paired. What does that mean? What could be reason for 0% properly mapped? I will greatly appreciate your input.
The proper pair status is read directly from the SAM record - it's the 0x2 bit in the FLAG field (the second token in a SAM record). See the SAM specification for more details.
Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT