Are all fragments properly aligned is this fragment

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Unformatted text preview: ;><<<<><7<;<<<>><< XM:i:0 XO:i:1 XG:i:2 0 8M2I27M = <;9<<5><<<<><<<>><<><>><9>><>>>9>>><> XM:i:0 XO:i:1 XG:i:2 17644 XT:A:R MD:Z:18^CA19 21469 XT:A:R MD:Z:35 -314 NM:i:2 -244 NM:i:2 The Alignment Column The Alignment Column Harves0ng Informa0on from SAM •  Query name, QNAME (SAM)/read_name (BAM). •  FLAG provides the following informa0on: –  are there mul0ple fragments? –  are all fragments properly aligned? –  is this fragment unmapped? –  is the next fragment unmapped? –  is this query the reverse strand? –  is the next fragment the reverse strand? –  is this the last fragment? –  is this a secondary alignment? –  did this read fail quality controls? –  is this read a PCR or op0cal duplicate? Bitwise Flags FLAG: bitwise FLAG. Each bit is...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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