1sam(5) Bioinformatics formats sam(5)
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6 sam - Sequence Alignment/Map file format
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9 Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the
10 header lines, which are started with the `@' symbol, each alignment
11 line consists of:
12 1 QNAME Query template/pair NAME
14 2 FLAG bitwise FLAG
15 3 RNAME Reference sequence NAME
16 4 POS 1-based leftmost POSition/coordinate of clipped sequence
17 5 MAPQ MAPping Quality (Phred-scaled)
18 6 CIGAR extended CIGAR string
19 7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
20 8 MPOS 1-based Mate POSition
21 9 TLEN inferred Template LENgth (insert size)
22 10 SEQ query SEQuence on the same strand as the reference
23 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
24 12+ OPT variable OPTional fields in the format TAG:VTYPE:VALUE
25 Each bit in the FLAG field is defined as:
27 0x0001 p the read is paired in sequencing
29 0x0002 P the read is mapped in a proper pair
30 0x0004 u the query sequence itself is unmapped
31 0x0008 U the mate is unmapped
32 0x0010 r strand of the query (1 for reverse)
33 0x0020 R strand of the mate
34 0x0040 1 the read is the first read in a pair
35 0x0080 2 the read is the second read in a pair
36 0x0100 s the alignment is not primary
37 0x0200 f the read fails platform/vendor quality checks
38 0x0400 d the read is either a PCR or an optical duplicate
39 0x0800 S the alignment is supplementary
40 where the second column gives the string representation of the FLAG
42 field.
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45 https://github.com/samtools/hts-specs
46 The full SAM/BAM file format specification
47htslib August 2013 sam(5)