Mapping quality repeat structure reads falling in

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Unformatted text preview: explained in the following table: Bitwise Representa0on 1 = 00000001 paired ­end read 2 = 00000010 mapped as proper pair 4 = 00000100 unmapped read 8 = 00001000 read mate unmapped 16 = 00010000 read mapped on reverse strand Example: The flag 11 1 + 2 + 8 = 00001011 (condi0ons 1, 2, 8) •  Flags 0, 4, and 16 are the flags most commonly used. The Alignment Column Mapping Quality •  Phred score, iden0cal to the quality measure in the fastq file. quality Q, probability P: P = 10 ^ ( ­Q / 10.0) •  If Q=30, P=1/1000on average, one of out 1000 alignments will be wrong •  As good as this sounds it is not easy to compute such a quality. Mapping Quality •  Repeat structure. Reads falling in repe00ve regions usually get very low mapping quality. •  Base quality of the read. Low quality means the observed read sequence is possibly wrong, and wrong sequence may lead...
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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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