question about bwa sam file

peachgil · 02-16-2011, 10:27 AM

Hi, Everyone

I used bwa samse to generate a sam file (all of setting are default, including index and aln steps), but I got some lines like this:

301 VHE-8239602811014-9-2-3-1761 16 uc008guk.1 3521 23 16M * 0 0 AGTGCTCAGAGATGTA * XT:A:U NM:i:1 X0:i:1 X1:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C2 XA:Z:uc009jck.1,-72,16M,2;

Since X0 means 'Number of best hits' based on bwa manual page, in my case, it's X0:i:1, this should be only one, but it does has XA field, XA:Z:uc009jck.1,-72,16M,2;, which means it has another best match. Any comment? Also, in XA field, -72 should be position, but why is that negative?

Thanks a lot

Gilbert

jiangyuehit · 04-06-2011, 09:53 AM

Hi Gibert

I guess the content in XA field refers to X1:i:1.

"-" means the strand, not a negative value.

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02-16-2011, 10:27 AM	#1
peachgil Junior Member Location: US Join Date: Feb 2011 Posts: 2	question about bwa sam file Hi, Everyone I used bwa samse to generate a sam file (all of setting are default, including index and aln steps), but I got some lines like this: 301 VHE-8239602811014-9-2-3-1761 16 uc008guk.1 3521 23 16M * 0 0 AGTGCTCAGAGATGTA * XT:A:U NM:i:1 X0:i:1 X1:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C2 XA:Z:uc009jck.1,-72,16M,2; Since X0 means 'Number of best hits' based on bwa manual page, in my case, it's X0:i:1, this should be only one, but it does has XA field, XA:Z:uc009jck.1,-72,16M,2;, which means it has another best match. Any comment? Also, in XA field, -72 should be position, but why is that negative? Thanks a lot Gilbert

04-06-2011, 09:53 AM	#2
jiangyuehit Junior Member Location: toronto Join Date: Apr 2011 Posts: 2	Hi Gibert I guess the content in XA field refers to X1:i:1. "-" means the strand, not a negative value.