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Old 09-06-2010, 03:32 AM   #1
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Location: Beijing, China

Join Date: Jun 2010
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Default BWA Uniquely Mapped Reads

Hello, everyone!
This is an alignment output I got from "bwa sampe", and as I know, "XT:A:U" means "reads uniquely mapped to reference", but I also got the alternative hits of "XA:...", why is that?? And if I only care about uniquely mapped reads, is this kind of reads what I want? Please help me out, Thanks A Lot!

d5_lpEsQulsn42 147 chr4 110995170 60 63M = 110995022 -211 TTTCTTTTGCCTGATTGCCCTGGCCAGAGCTTCCAATACTGTGTTGAATAGGAGTGGTGAGAG __aYbaaa_c_bbabWaa`_\bbbbabb`bbbbbbbbbabbbbbbbbbbbbbbbbbbbbbbbb XT:A:U NM:i:0 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:63 XA:Z:chr11,-121159338,63M,1;

Last edited by NF_seq; 09-06-2010 at 03:38 AM.
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