samtools idxstats showing accession number and genomic scaffold

Question

[whb]

Hi,

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 read-segments.

But why do I have have four columns in some?

Samtools idxstats file.bam

multiple image

Answer 1

[Pierre Lindenbaum]

Is this an expected output for Samtools idxstats?

yes if those accession numbers were used as the name of the chromosomes in the reference genome....

you can check this using

samtools view -H your.bam | grep '^@SQ'