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3 hours ago by


Is this an expected output for Samtools idxstats? Why is it showing accession instead of chromosome number? most of the NC_... corresponds to a chromosome but why do I have NT and NW genomic scaffold?

Samtools Manuel :

output is TAB-delimited with each line consisting of reference
sequence name, sequence length, # mapped read-segments and # unmapped

But why do I have have four columns in some?

Samtools idxstats file.bam

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