What is mean that mpileup read depth (read count) 0?

Question

[Peavil]

Hi,

I finish preprocess a bam file like base recalibrator, mark duplicate, ... and then, I run samtools mpileup with the bam.

Most are in the form below.

chr1    1007432 g       30      .$,$.,,..AAa,.AAa,,AA.aAa.A..,a,        3>5>;::@]<>::==>>4E6>>=8876@6<

But, I could see rows that read depth is 0

chr6    32551911        C       0
chr6    32610535        A       0

How can I interpret read count is 0 data in mpileup result? (I already run IGV and, pick that position. As a result, there is no read)

Thanks for reading this story.

Answer 1

[Devon Ryan]

There are no alignments there, that's all that it means.

[Peavil]

thank you. I think I was mistaken for a while!