A dot means a match on the forward strand and a comma a match on the reverse strand, so there's no difference (aka mismatch) in either read covering that position. The last column is indeed Phred score + 33.
FYI, if you were to input multiple BAM files, you'd find the output similar, with some of the columns repeated for each of the samples. Devon ____________________________________________ Devon Ryan, Ph.D. Email: [email protected] Tel: +49 (0)178 298-6067 Molecular and Cellular Cognition Lab German Centre for Neurodegenerative Diseases (DZNE) Ludwig-Erhard-Allee 2 53175 Bonn, Germany On Aug 4, 2014, at 10:21 PM, Thiago M. Venancio wrote: > Hi Devon and TNP, > > Thanks for the feedback. Please allow me one clarification to see if I > understood the documentation correctly. > > Thanke the following row from my example: > > supercontig_0 32 C 2 ., BH > > This means that at supercontig_0 we have a reference C at position 32, with > two mapped reads with potential SNPs. However, dot and comman means > differences between reads and each strand of the reference sequence. So, if > the sequencing method is not strand specific, these SNPs should be excluded. > Am I missing something or this point is correct ? > > Finally, how the last column (base quality) should be interpreted ? Should I > use the ASCII of the character minus 33 ? > > Sorry if these questions are very basic. I am just trying to make sure I > understood the process. > > Best, > Thiago > > > > > On Mon, Aug 4, 2014 at 5:00 PM, Devon Ryan <[email protected]> wrote: > Hi Thiagp > > The format, including the last 3 columns is described here: > http://samtools.sourceforge.net/pileup.shtml > > Best, > Devon > > ____________________________________________ > Devon Ryan, Ph.D. > Email: [email protected] > Tel: +49 (0)178 298-6067 > Molecular and Cellular Cognition Lab > German Centre for Neurodegenerative Diseases (DZNE) > Ludwig-Erhard-Allee 2 > 53175 Bonn, Germany > > On Aug 4, 2014, at 9:48 PM, Thiago M. Venancio wrote: > > > Hi all, > > > > I ran the samtools mpileup on a set of mapped reads (in bam format). The > > output gave me something like that: > > > > supercontig_0 30 T 2 ^g.^g, BH > > supercontig_0 31 G 2 ., AG > > supercontig_0 32 C 2 ., BH > > supercontig_0 1689 T 4 .,^g.^g, GBA5 > > supercontig_0 1690 A 4 .,., GBAD > > supercontig_0 1691 A 4 .,., BAAF > > supercontig_0 1692 C 4 .$,$., EA?C > > > > I inspected all the documentation I could find over the past few hours and > > was unable to find a complete explanation for this output. I understand > > the first three columns, but not the other three. > > > > Can anyone point me the appropriate documentation ? > > > > Thanks in advance. > > Thiago > > ------------------------------------------------------------------------------ > > Infragistics Professional > > Build stunning WinForms apps today! > > Reboot your WinForms applications with our WinForms controls. > > Build a bridge from your legacy apps to the future. > > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk_______________________________________________ > > Samtools-help mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/samtools-help > > > > > -- > ================================= > Thiago Motta Venancio, M.Sc., PhD > http://venancio.openwetware.org/ > ================================= ------------------------------------------------------------------------------ Infragistics Professional Build stunning WinForms apps today! Reboot your WinForms applications with our WinForms controls. Build a bridge from your legacy apps to the future. http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
