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sam(5)			    Bioinformatics formats			sam(5)

       sam - Sequence Alignment/Map file format

       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 POSition
	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

	      The full SAM/BAM file format specification

htslib				  August 2013				sam(5)


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