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Merge pull request #1014 from cfe-lab/update-steps-docs-on-nuc
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docs: describe genome.pos field of nuc.csv output
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donkirkby authored Sep 12, 2023
2 parents 5d1e826 + cf67615 commit 3f791c5
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Expand Up @@ -322,6 +322,10 @@ Individual files are described after the list of steps.
contig that the reads were mapped to
* refseq.nuc.pos - the 1-based index of the base in the coordinate reference
for a single gene region on non-coding region, named in the region column
* genome.pos - the absolute 1-based index of a nucleotide (in other words,
relative to the beginning of the entire reference sequence). This is the same
as refseq.nuc.pos, but not specific to a single gene or
non-coding region.
* A,C,G,T - counts for the nucleotides at this position
* N - count of reads with Phred quality score below the cutoff
* del - count of reads with a deletion at this position
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