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?