Hi I am seeing some inconsistency in the samtools mpilup. It seems to report a mix of phred + 33 and phred + 64 for the basequality in a .bam file. However when viewing the same .bam file using samtools view it appears to only use phred +33.
I am using samtools/1.8 Eksample: $samtools mpileup -r 1:43149119-43149119 -q 0 -Q 0 -f Hg19.fasta sample.bam 1 43149119 G 214 .$.$.....,.,,..,.,..,...,,.,,.,...,....,,a...,...,..,.A,.,,,,,,,,..,,...,,,,....,,,.,,....,,,.,.,,,,.,,,.a,,.,...,....,,,..,,,,,.,,.A,,.,,..,,.,,A..,,,,,...,,.,,,,..,.,,,,,,,,,.a,.,,,.,,,,,,,,.,,,,,.,.,,,,,,,,,,,,,,, b>^?=_=@=??]@A^AAbBBccBAcBBcB<LcBBBcBAA>BcBAABcBBcAb,AcCBC,CBBCddCBBBdCCCBcBBBACCBBC?cdBC!8A!c!C!CBBCBB?CC7CABA!aaAB@B!Bc!CCBC;CCABC!cCBAB!CB!BBd@B!?CB@ABC!A!CC!B`Bb!C!!!!!CCA?B<CC!BBCCCCCCCAC!CCAACA!A!!!!!!A!=!=A! Here I observe the ascii characters : "^","]","b","c" which belongs to phred + 64 and the remaining characters are from phred + 33. $samtools view sample.bam "1:43149119-43149119 Inspecting visually the output of this command I cannot find any phred +64 ascii characters such as lower-case lettters in the column containing the basequality string. Subset of the basequality column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thought it was odd to find a mix of phred +33 and phred +64 as this bam file was sequenced in 2018 and it was expected to have only phred +33 values. Please let me know if you need more info Regards Karina
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