What Are The > Signs In Samtools Pileup Strings?

Question

[Z Z]

e.g.:

1       554617  N       18      >>TTttTTTTTTTTTTTT      FJFFIJJHI2JI?JJFCC

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

Thanks!

Answer 1

[Pierre Lindenbaum]

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

[Gvj]

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

[Pierre Lindenbaum]

it's a deletion in the read.

REF     ===================================
READ  =============.......===================

Answer 2

[Damian Kao]

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

The symbols are base quality.

[Z Z]

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

[Damian Kao]

I see. My mistake.