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1 '\" t
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2 .TH sam 5 "August 2013" "htslib" "Bioinformatics formats"
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3 .SH NAME
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4 sam \- Sequence Alignment/Map file format
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5 .\"
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6 .\" Copyright (C) 2009, 2013 Genome Research Ltd.
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7 .\"
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8 .\" Author: Heng Li <lh3@sanger.ac.uk>
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9 .\"
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10 .\" Permission is hereby granted, free of charge, to any person obtaining a
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11 .\" copy of this software and associated documentation files (the "Software"),
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12 .\" to deal in the Software without restriction, including without limitation
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13 .\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
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14 .\" and/or sell copies of the Software, and to permit persons to whom the
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15 .\" Software is furnished to do so, subject to the following conditions:
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16 .\"
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17 .\" The above copyright notice and this permission notice shall be included in
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18 .\" all copies or substantial portions of the Software.
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19 .\"
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20 .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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21 .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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22 .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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23 .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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24 .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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25 .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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26 .\" DEALINGS IN THE SOFTWARE.
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27 .\"
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28 .SH DESCRIPTION
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29 Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started
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30 with the `@' symbol, each alignment line consists of:
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31 .TS
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32 nlbl.
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33 1 QNAME Query template/pair NAME
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34 2 FLAG bitwise FLAG
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35 3 RNAME Reference sequence NAME
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36 4 POS 1-based leftmost POSition/coordinate of clipped sequence
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37 5 MAPQ MAPping Quality (Phred-scaled)
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38 6 CIGAR extended CIGAR string
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39 7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
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40 8 MPOS 1-based Mate POSistion
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41 9 TLEN inferred Template LENgth (insert size)
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42 10 SEQ query SEQuence on the same strand as the reference
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43 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
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44 12+ OPT variable OPTional fields in the format TAG:VTYPE:VALUE
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45 .TE
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46 .PP
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47 Each bit in the FLAG field is defined as:
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48 .TS
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49 lcbl.
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50 0x0001 p the read is paired in sequencing
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51 0x0002 P the read is mapped in a proper pair
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52 0x0004 u the query sequence itself is unmapped
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53 0x0008 U the mate is unmapped
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54 0x0010 r strand of the query (1 for reverse)
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55 0x0020 R strand of the mate
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56 0x0040 1 the read is the first read in a pair
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57 0x0080 2 the read is the second read in a pair
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58 0x0100 s the alignment is not primary
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59 0x0200 f the read fails platform/vendor quality checks
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60 0x0400 d the read is either a PCR or an optical duplicate
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61 0x0800 S the alignment is supplementary
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62 .TE
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63 .P
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64 where the second column gives the string representation of the FLAG field.
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65 .SH SEE ALSO
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66 .TP
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67 https://github.com/samtools/hts-specs
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68 The full SAM/BAM file format specification
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