[Samtools-help] Consensus Pileup Extra Columns

[Paige T. <spt...@uc...>]

Hi,

I have a question concerning the columns generated in consensus pileups.  Here are a few rows from my pileup:

chr1	383	*	+C/*	727	727	13	88	+C	*	13	74	1	21	16
chr1	443	*	-t/*	750	1110	35	84	-t	*	5	79	0	0	0
chr1	603	g	R	99	99	37	36	A$.AA.,,.,.,a...a,,,..,a.,,,..A,aA,,.	/V"EK`^M`"``<OF_[VDZWDXL7`"<`[=IW<*`
chr1	684	t	A	13	20	37	3	.aa	T7I

For indels, 15 columns are printed. The manual page and FAQ (http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_FAQ) describes the first 13 columns, but I am wondering what the last two columns represent?  

Thank you, 

Paige


Paige Taylor
spt...@uc...
Ph.D. student, Stanley Nelson Lab
Gonda 5554
University of California, Los Angeles