sam(5)

Sequence Alignment/Map file format

Section 5 libhts3 bookworm source

Description

sam

NAME

sam - Sequence Alignment/Map file format

DESCRIPTION

Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started with the ‘@’ symbol, each alignment line consists of:

Image grohtml-37407-1.png

Each bit in the FLAG field is defined as:

Image grohtml-37407-2.png

where the second column gives the string representation of the FLAG field.

SEE ALSO

https://github.com/samtools/hts-specs

The full SAM/BAM file format specification