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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 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

       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)