sam/ bam bitwise FLAGs

Flag (bin)Flag (hex)Meaning
10x1Paired-end sequence (or multiple-segment, as in stroble sequencing)
20x2Aligned in proper pair (according to the aligner)
40x4Unmapped
80x8Mate pair unmapped (or next segment, if multipe-segment)
160x10Sequence is reverse complemented
320x20Sequence of mate pair is reversed
640x40The first read in the pair (or segment, if multiple-segment)
1280x80The second read in the pair (or segment, if multiple-segment)
2560x100Secondary alignment
5120x200QC failure
10240x400PRC or optical duplicate
20480x800Supplementary alignment

See SAMv1 specs

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