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.TH sam 5 "August 2013" "htslib" "Bioinformatics formats"
.SH NAME
sam \- Sequence Alignment/Map file format
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.\" Copyright (C) 2009, 2013 Genome Research Ltd.
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.\" Author: Heng Li <[e-mail]>
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.SH 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:
.TS
nlbl.
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
.TE
.PP
Each bit in the FLAG field is defined as:
.TS
lcbl.
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
.TE
.P
where the second column gives the string representation of the FLAG field.
.SH SEE ALSO
.TP
https://github.com/samtools/hts-specs
The full SAM/BAM file format specification