1sam(5)                      Bioinformatics formats                      sam(5)
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NAME

6       sam - Sequence Alignment/Map file format
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DESCRIPTION

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:
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13        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 POSistion
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
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26       Each bit in the FLAG field is defined as:
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28       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
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41       where  the  second  column  gives the string representation of the FLAG
42       field.
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SEE ALSO

45       https://github.com/samtools/hts-specs
46              The full SAM/BAM file format specification
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50htslib                            August 2013                           sam(5)
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