Question: PE read flag 69 and 137 meaning
0
4.2 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
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 • 1.1k views
modified 4.2 years ago by harold.smith.tarheel4.6k • written 4.2 years ago by epigene490
3
4.2 years ago by
United States
harold.smith.tarheel4.6k wrote: