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What Are The > Signs In Samtools Pileup Strings?

e.g.:

1       554617  N       18      >>TTttTTTTTTTTTTTT      FJFFIJJHI2JI?JJFCC

what is ">>" in the base reads part ">>TTttTTTTTTTTTTTT"?

Thanks!

samtools pileup
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by Z Z • Z Z

2 answers

I think it is the symbol for "reference skip" (indel)

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written by Pierre Lindenbaum Pierre Lindenbaum

But, Do you know what does make it to skip ? I see that read quality is good there and only few reads skipped .

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written by Gvj Gvj

it's a deletion in the read.

REF     ===================================
READ  =============.......===================
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written by Pierre Lindenbaum Pierre Lindenbaum

Here is a description of the pileup format: http://samtools.sourceforge.net/pileup.shtml

The symbols are base quality.

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written by Damian Kao Damian Kao

As I understand, base qualities is "FJFFIJJHI2JI?JJFCC" string. I'm asking about > sign in read bases string ">>TTttTTTTTTTTTTTT".

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written by Z Z • Z Z

I see. My mistake.

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written by Damian Kao Damian Kao

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