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Question about FIELD information in samtools

Hi all.

I am using the samtools to annotate my variants information and also am trying to use the I16 Field provided by samtools.

You can see its manual at http://samtools.sourceforge.net/mpileup.shtml

There are a total of 16 independent values in I16 field and first one is "#reference Q13 bases on the forward strand".

I almost understood the meaning of definition above statement but ,in order to better understand, I posted here!

I think that definition of Q13 is quality score 13. Or is that indicating the number of reads that are more than quality score of 13?

I am confused.

On top of that, what is the tail distance? Although I tried to find detailed information about the I16 field, but I failed.

Thanks

sequence next-gen-sequencing
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updated by Ram Ram • written by mangfu100 mangfu100

Q13 is a quality score of at least 13 (i.e., >=13).

Perhaps "tail distance" is the distance to the end of the read, but that's just a guess (thus why this is a comment).

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written by Devon Ryan Devon Ryan

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