What second field zero means in sam file?
Number_of_reads FLAG_bitwise_FLAG
153306 0
556844 16
I know 16 means 'read mapped in reverse strand' Does zero means read is unmapped? Can't in any assignment here for zero values
https://broadinstitute.github.io/picard/explain-flags.html
Here is one example:
HISEQ-MFG:98:HHYW2BCXX:1:1107:16275:82472 0 gi|255767013|ref|NC_000964.3| 2409764 60 100M * 0 0 TATTGCATGCGGCGCTTGCGGAGCTGCTGCACCAGACATTTACGATTACGATGATGAAGGCATCGCGTTCGTAACGCTTGATGAAAACAAAGGTGTTGTC DDDDDIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIHEHHIIIIII NM:i:0 MD:Z:100 AS:i:100 XS:i:0
The read has mapping quality of 60, good value, but has zero for FLAG bitwise FLAG. What does it means?
1 answer
None of the flags is checked so
- read paired == FALSE = The read is part of a single-end experiment (so flags like mate_xxxx, properly paired, first in pair are meaningless )'
- read unmapped == FALSE = The read is mapped on a contig/chromosme
- reverse strand == FALSE = The read is mapped on + strand
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Pierre Lindenbaum
please, read my answer again
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Pierre Lindenbaum
The read is not paired, not unmapped and not on the reverse strand. Therefore the reads is from a SE experiment, therefore the read is mapped, therefore the read is on the + strand.
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WouterDeCoster
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