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Man Pages


Manual Reference Pages  -  SAM (5)

NAME

sam - Sequence Alignment/Map file format

CONTENTS

Description
See Also

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:

1QNAMEQuery template/pair NAME
2FLAGbitwise FLAG
3RNAMEReference sequence NAME
4POS1-based leftmost POSition/coordinate of clipped sequence
5MAPQMAPping Quality (Phred-scaled)
6CIGARextended CIGAR string
7MRNMMate Reference sequence NaMe (‘=’ if same as RNAME)
8MPOS1-based Mate POSistion
9TLENinferred Template LENgth (insert size)
10SEQquery SEQuence on the same strand as the reference
11QUALquery QUALity (ASCII-33 gives the Phred base quality)
12+OPTvariable OPTional fields in the format TAG:VTYPE:VALUE

Each bit in the FLAG field is defined as:

0x0001pthe read is paired in sequencing
0x0002Pthe read is mapped in a proper pair
0x0004uthe query sequence itself is unmapped
0x0008Uthe mate is unmapped
0x0010rstrand of the query (1 for reverse)
0x0020Rstrand of the mate
0x00401the read is the first read in a pair
0x00802the read is the second read in a pair
0x0100sthe alignment is not primary
0x0200fthe read fails platform/vendor quality checks
0x0400dthe read is either a PCR or an optical duplicate
0x0800Sthe 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
Search for    or go to Top of page |  Section 5 |  Main Index


htslib SAM (5) August 2013

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