Code:
HWI-ST314:228:C1NU0ACXX:6:2205:3950:78621 99 chr1 315318847 29 10M1D12M14S chr2 3874 0 GGATGGGGTGAAGCTGGAGGATAGGCGCCCCATCTG IJJIJJJJJJJJJJJJJJJJIJJHHHGHFFFFFCCC XT:A:M NM:i:5 SM:i:29 AM:i:29 XM:i:4 XO:i:1 XG:i:1 MD:Z:2C2T4^C1G6A3 HWI-ST314:228:C1NU0ACXX:6:2205:3950:78621 147 chr2 3874 29 36M chr1 315318847 0 CCATGAGGCACAGGCGGTAGCATTCAGGGCAGTGCC CCCFFFFFHHHHHGJJJGHIIIJIJJJJJIJIJIIJ XT:A:U NM:i:0 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36
read paired
read mapped in proper pair
mate reverse strand
first in pair
Flag 147:
read paired
read mapped in proper pair
read reverse strand
second in pair
How can they map on different chromosomes (chr1 and chr2) and still qualify as "proper pair"? While most of the "proper pairs" in this file do map on the same target (and in a convergent orientation, with an insert size in the expected range), I do not understand a couple of them...
Thanks for any comment.