sam (5) Linux Manual Page
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 POSition |
| 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