FLAG

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Current specifications for the FLAG column in a SAM/BAM file can be found at [1].

In plain English, the following table represents the value that is used in the FLAG column. Adding these values up will give you the total value used in the FLAG column.

FlagType Flag Value
ReadIsPaired 1
ReadIsMappedInPair 2
QueryIsUnmapped 4
MateIsUnmapped 8
ReverseStrand 16
ReverseMateStrand 32
ReadIsFirstInPair 64
ReadIsSecondInPair 128
AlignmentIsSecondary 256
ReadIsFailed 512
ReadIsDuplicate 1024