Question: What second field zero means in sam file?
1
gravatar for biotech
2.8 years ago by
biotech540
United States
biotech540 wrote:
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?

sam • 1.2k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by biotech540
1
gravatar for Pierre Lindenbaum
2.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

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
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Pierre Lindenbaum124k

I don't understand your answer Pierre.

ADD REPLYlink written 2.8 years ago by biotech540
2

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.

ADD REPLYlink written 2.8 years ago by WouterDeCoster42k
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