1k genomes .bam qualities

[keebs42]

Hi,
Anyone familiar with the 1k genomes pilot 2 alignment .bam files? I'm wondering if the base qualities given (after converting to pileup) are Solexa/Illumina scaled.

thanks,
Jonathan

[lh3]

SAM/BAM always uses the Sanger-like qualities throughout.

[SH1]

last column of pileup

Hello - This may be a naive question, but what do the Sanger-like qualities mean? The pileup page talks extensively about the base read column, but I can't seem to find information on the last column (bolded below). Is this some sort of standard formatting that I'm unaware of? Thanks for any help - I'm very new to NGS analysis.

seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&