Entering edit mode
6 months ago
mk-dna
•
0
Hi,
I am working with an mpileup file generated via Popoolation2. All my data is paired-end pooled WGS derived from 24 unique populations.
I want to filter my file to only include positions with a read depth of >5. Is the read depth represented only once for all populations in the file (4th column), or is there a read depth value for each population?
I couldn't find any information on columns >6 online, and there are 24 integers in my data (aside from column 2), followed by what appear to be unique base info & quality scores. Please let me know what those later columns mean, and what the deal is with read depth!
Thanks!!
Also, here is an output from a single row:
chrI 88 G 90 .......................,,,,.,,.,..,...,...,..,.,,...,,.......,...,......,..............,,. FFFFFkFkFFF:FFFFFFFF:FFkFkkFkkF_:Fkk_FFkFF_kFkkFkFFFkkkFFF:kFkFFFkFFFFFFkkFFFkFFFkFFF:FFkkF 69 ..................,,,,,,,...,...........,....,.....,,,,....,.....,,^], FFkkF_FFFkFFFkFFF:QkFFFkkFFFkFFkFFFFFF:FFkkFFkkFFFkFkFFkkFkFkFFFFFkkk 72 ...............,,,,,,,........,....,,....,.........,....,..,,...^].^]. kFF:FF_Fk:FkFFFF:kFFFFkkFFFFFFFkkFFFkFFFFFFFFFFFFFFFFFFFkFFFFkFkFkFFFF:F 65 ......................,,,....,.....,,.,,......,,,....,...,........^].^]. FFFFFFFkFFFFkFFkFkFFFFF:FkFFFFFFkFkFkkFFFFkFFFFFFFFFFkF:FFFFFFFF 61 ...A..............A.,,,....,,................,...,.,..,..,,,. kFkFFFk:FFFFFFFFFFFFFF_FFFF_FFFF:FFFFFFFFFFFFkF:Fk:kFF:FkFkF 62 ..................,,,...,....,..,....,........,.....,,,,,...., kFFFFkFFkkFkFFF:FFFkFFFkFFFFFFFFFFFkFk:FFkFFFFkFF:FFkFFFFFFFFk 58 .........,,,,,,,.......,..............,,,.........,....,, _FFFFFQFFFkkkFFkkFFFFkFFkFFF:FFFkkFFFFFkkk:FF:kFFkFkkkFFkF 60 ................,,.....,.,.....,....,.,.,....,......,,...., kFFFFFFkkFFkkFFkFFFFFFkFFFFFFFFFkFFFFFFFFkFFFFkF:FFFFkFFFFFk 53 ..........,,..,....,,....,,.....,....,............. kFFFFkFFkkkFF:FkFkFFkFFFFFkkFFFFFFFkF:FkFFFFFFFFFFFkF 59 ...........,,,,,,,,,...,.,,,,,,,...,.,.,......,...,.,..... FkFkFkk::FkkFFkFFQkk_FFkkkkkkkkkkFkFkFkFkkFQFFFkFQkFFkFFFkk 44 .........$..,,,,,.....,......,.........,.., FFFF:>FFFkk:FkkkFQFFFFFFFFFFFFFFkFkFFFFFFFFFk 34 .................,...,..........^]. FFkFFF_kkFFFFFFkkFFFFFkFFFFFFFFFF: 6 .,.,^]. TFkFFB 16 .....,.,.,...,,^]. T<F=FcTF<FFFF/B 12 ,,.,....,,,. FFBFgF<B//BB 22 ...**,,,,,,...,....,., /JTFFFFFFF/FFFkFF/FBF7 15 ,,,..*.......,^]. FFFFFFFFFFFF<gB 12 .,,,.,...,.. ]FFFFFF/FF<F 8 .,,.,.,. /kF=><FF 15 .,..,....,...^].^]. /FFPF/FFFgFB<B/ 17 ..,,.,....,.,...^]. /TFF/F]/FFFFFFFFB 11 ..,,,,,.,.. akFBFFFFJFB 7 .....,^]. FFFFBTB 10 .,....,... TFE=<FFFFB
