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  • syfo
    started a topic a trans-chromosomal "proper pair"?

    a trans-chromosomal "proper pair"?

    How could two reads define a "proper pair" when they do not map on the same target? Here are the bam entries I do not understand (from bwa):

    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
    Flag 99:
    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.

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