Question: PE read flag 69 and 137 meaning
0
gravatar for epigene
3.4 years ago by
epigene490
United States
epigene490 wrote:

I'm very confused with the meaning of flag 69 and 137. From the explain flag tool https://broadinstitute.github.io/picard/explain-flags.html

flag 69 (1+4+64) means:

    read paired
    read unmapped
    first in pair

flag 137 (1+8+128) means:

    read paired
    mate unmapped
    second in pair

Here is one example of the alignment pair where I rename the ID to xxx:8292:

xxx:8292    69      chr1    63020   0       *       =       63020   0       GGCGCACGAAAAACGCGAAAGCGTTTCACGATAAATGCGAAAACATACGGTACGGTCTATCATGTTCCATCTCATCCCTGCGTTTCTCCG        C<CCCEFGGDCFFGEEEGGEGFGGGE<FEF@FC@@EDA@FGGGFGEGG8,CDCCGFFGGGGG9CFFFCF?CEFGGGF8EFGGG,FFGGGC        PG:Z:MarkDuplicates     AS:i:0  XS:i:0
xxx:8292    137     chr1    63020   60      8S44M   =       63020   0       CAAACCTAAAACCTTTTTTACAATTGGCCTACCAATCGAGCGATGTTTTGAG      A----6;-C<,,BFEFG,@,;,,6C,,;,@,C@86<C8E@,+7,,6,<C,B@    MD:Z:35G8       PG:Z:MarkDuplicates     NM:i:1  AS:i:39 XS:i:0
^C

What I'm confused is, based on the flag, it seems to me that both read 1 and read 2 from this pair of PE reads are unmapped since flag 4 is set for read 1 and flag 8 is set for read 2 and flag 4 and 8 means read and mate unmapped respectively. Then is this read pair mapped? or is read 1 mapped? or read 2 mapped?

From this post, http://seqanswers.com/forums/showthread.php?t=17314, it suggests the alignment with flag 137 is mapped, consistent with the actual alignment example. But isn't flag 8 (mate unmapped) set? Could someone help me clarify my confusion?

Thanks!

sam flag • 1.0k views
ADD COMMENTlink modified 3.4 years ago by harold.smith.tarheel4.5k • written 3.4 years ago by epigene490
3
gravatar for harold.smith.tarheel
3.4 years ago by
United States
harold.smith.tarheel4.5k wrote:

Read 1 is unmapped, read 2 is mapped. Flag 8 for read 2 means it's mate (read 1) is unmapped.

ADD COMMENTlink written 3.4 years ago by harold.smith.tarheel4.5k

thanks for the answer, I was apparently confused with the meaning of flag 4 and 8.

ADD REPLYlink written 3.4 years ago by epigene490
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