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sam(5) Bioinformatics formats 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 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 htslib August 2013 sam(5)
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