I have a pileup format file for a particular accession SRR1011475.
This pileup format file was obtained using NCBI sratoolkit.
MT_H37RV_BRD_V5 750 C 1 ^~, # MT_H37RV_BRD_V5 751 C 1 , # MT_H37RV_BRD_V5 752 G 1 , # MT_H37RV_BRD_V5 753 C 1 , # MT_H37RV_BRD_V5 754 G 1 , #
But I am unable to figure out which reference sequence was used to build up this pileup format file?
When I downloading the bam file for this particular accession SRR1011475 and try to generate the pileup file format using [Generate pileup from BAM dataset (Galaxy Version 1.1.2), using samtool], with my reference then I get N bases.
MT_H37RV_BRD_V5 750 N 1 ^~c # ~ MT_H37RV_BRD_V5 751 N 1 c # ~ MT_H37RV_BRD_V5 752 N 1 g # ~ MT_H37RV_BRD_V5 753 N 1 c # ~ MT_H37RV_BRD_V5 754 N 1 g # ~
why is this difference coming in both the files? please suggest a way