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- .TH sam 5 "August 2013" "htslib" "Bioinformatics formats"
- .SH NAME
- sam \- Sequence Alignment/Map file format
- .SH 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:
- .TS
- nlbl.
- 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
- .TE
- .PP
- Each bit in the FLAG field is defined as:
- .TS
- lcbl.
- 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
- .TE
- .P
- where the second column gives the string representation of the FLAG field.
- .SH SEE ALSO
- .TP
- https://github.com/samtools/hts-specs
- The full SAM/BAM file format specification
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