lecture3

# Mapping quality repeat structure reads falling in

This preview shows page 1. Sign up to view the full content.

This is the end of the preview. Sign up to access the rest of the document.

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...
View Full Document

## 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.

Ask a homework question - tutors are online