sam(5)

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:
1 | QNAME | Query template/pair NAME
2 | FLAG | bitwise FLAG
3 | RNAME | Reference sequence NAME
4 | POS | 1-based leftmost POSition/coordinate of clipped sequence
5 | MAPQ | MAPping Quality (Phred-scaled)
6 | CIGAR | extended CIGAR string
7 | MRNM | Mate Reference sequence NaMe (`=' if same as RNAME)
8 | MPOS | 1-based Mate POSistion
9 | TLEN | inferred Template LENgth (insert size)
10 | SEQ | query SEQuence on the same strand as the reference
11 | QUAL | query QUALity (ASCII-33 gives the Phred base quality)
12+ | OPT | variable OPTional fields in the format TAG:VTYPE:VALUE

Each bit in the FLAG field is defined as:
0x0001 | p | the read is paired in sequencing
0x0002 | P | the read is mapped in a proper pair
0x0004 | u | the query sequence itself is unmapped
0x0008 | U | the mate is unmapped
0x0010 | r | strand of the query (1 for reverse)
0x0020 | R | strand of the mate
0x0040 | 1 | the read is the first read in a pair
0x0080 | 2 | the read is the second read in a pair
0x0100 | s | the alignment is not primary
0x0200 | f | the read fails platform/vendor quality checks
0x0400 | d | the read is either a PCR or an optical duplicate
0x0800 | S | the alignment is supplementary

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