Hi all

I got pair-end Miseq data. and looking at the SAM file I got strange results:

as i understand a QNAME should appear once (if no pair) or twice (in both pairs) but not 3 times? (I bring 3 rows from the data)

can one explain this results?

M01015:3:000000000-A30BE:1:1112:17179:12693 99 chrI 173 60 25M = 230 82 CTCCGAACCACCATCCATCCCTCTA AAAAAAABDDDDDEEEGGGGGGIII RG:Z:3 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:25 XA:Z:chrII,+5961,25M,1;

M01015:3:000000000-A30BE:1:1112:17179:12693 99 chrI 173 60 25M = 230 82 CTCCGAACCACCATCCATCCCTCTA AAAAAAABDDDDDEEEGGGGGGIII RG:Z:3 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:25 XA:Z:chrII,+5961,25M,1;

M01015:3:000000000-A30BE:1:1112:17179:12693 147 chrI 230 60 25M = 173 82 TTACCCATATCCAACCCACTGCCAC HFCGGGGGGBDDDBDDDB?B????? RG:Z:3 XT:A:U NM:i:0 SM:i:37 AM:i:23 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:25

The first two are identical and only the third is the paired end read of the previous two.

Best,

yishai

I got pair-end Miseq data. and looking at the SAM file I got strange results:

as i understand a QNAME should appear once (if no pair) or twice (in both pairs) but not 3 times? (I bring 3 rows from the data)

can one explain this results?

M01015:3:000000000-A30BE:1:1112:17179:12693 99 chrI 173 60 25M = 230 82 CTCCGAACCACCATCCATCCCTCTA AAAAAAABDDDDDEEEGGGGGGIII RG:Z:3 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:25 XA:Z:chrII,+5961,25M,1;

M01015:3:000000000-A30BE:1:1112:17179:12693 99 chrI 173 60 25M = 230 82 CTCCGAACCACCATCCATCCCTCTA AAAAAAABDDDDDEEEGGGGGGIII RG:Z:3 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:25 XA:Z:chrII,+5961,25M,1;

M01015:3:000000000-A30BE:1:1112:17179:12693 147 chrI 230 60 25M = 173 82 TTACCCATATCCAACCCACTGCCAC HFCGGGGGGBDDDBDDDB?B????? RG:Z:3 XT:A:U NM:i:0 SM:i:37 AM:i:23 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:25

The first two are identical and only the third is the paired end read of the previous two.

Best,

yishai

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