<h2>UPDATE:</h2>
<p>Seeing a different question where similar vocabulary is used: it would not be one <em>strand</em> that would be lost. single stranded DNA is not very happy in the nucleus, and would either lead to something seriously bad or be gap-filled to make it dsDNA again.</p>
<p>It would instead be that one of two chromosomes has a deletion at that position, which would be a classic CNV.</p>
<h2>ORIGINAL ANSWER:</h2>
<p>No.</p>
<p>There are a variety of copy number variant (CNV) calling tools that put a lot of effort into statistically robust ways of asking this question, all of which are a lot more complex than just looking at raw coverage. <a href="https://www.nature.com/articles/s41598-021-93878-2" rel="nofollow noreferrer">I'd recommend looking more into them</a>.</p>
<p>In terms of explanations for lower coverage in some regions that aren't CNVs: sequenceability of DNA is not even, replication of DNA is not even, mappability of reads is not even, etc. You need to reject those hypotheses before you go to variants.</p>

CC BY-SA 4.0
2023-12-22T19:07:08.987Z
2023-12-22T19:17:48.797Z
2023-12-22T19:17:48.797Z
Maximilian Press
<p>This is a BAM file from a 30x coverage Nebula Genomics test opened with IGV.</p>
<p>I found an area (1:30169255-30169600) where the coverage is less than 15x. Can I interpret it as a part of one strand of Chromosome 1 is missing?</p>
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<wgs><indel><igv><chromosomes>
Can I interpret 15x coverage area as a part of one strand is missing?
# Can I interpret 15x coverage area as a part of one strand is missing?

(Asked by: username_0 on 2023-12-22)

This is a BAM file from a 30x coverage Nebula Genomics test opened with IGV.

I found an area (1:30169255-30169600) where the coverage is less than 15x. Can I interpret it as a part of one strand of Chromosome 1 is missing?

[![enter image description here](https://i.sstatic.net/glhOQ.png)](https://i.sstatic.net/glhOQ.png)

[![enter image description here](https://i.sstatic.net/3awb4.png)](https://i.sstatic.net/3awb4.png)

**Tags:** wgs, indel, igv, chromosomes

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## 1 answers

### Answer by username_1 on 2023-12-22. Score: 1

## UPDATE:

Seeing a different question where similar vocabulary is used: it would not be one *strand* that would be lost. single stranded DNA is not very happy in the nucleus, and would either lead to something seriously bad or be gap-filled to make it dsDNA again.

It would instead be that one of two chromosomes has a deletion at that position, which would be a classic CNV.

## ORIGINAL ANSWER:

No.

There are a variety of copy number variant (CNV) calling tools that put a lot of effort into statistically robust ways of asking this question, all of which are a lot more complex than just looking at raw coverage. [I'd recommend looking more into them](https://www.nature.com/articles/s41598-021-93878-2).

In terms of explanations for lower coverage in some regions that aren't CNVs: sequenceability of DNA is not even, replication of DNA is not even, mappability of reads is not even, etc. You need to reject those hypotheses before you go to variants.


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