Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-12-22T19:07:08.987Z
Answers.LastActivityDate: 2023-12-22T19:17:48.797Z
Answers.LastEditDate: 2023-12-22T19:17:48.797Z
Answers.UserDisplayName: Maximilian Press
Body: <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>
  <p><a href="https://i.sstatic.net/glhOQ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/glhOQ.png" alt="enter image description here" /></a></p>
  <p><a href="https://i.sstatic.net/3awb4.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/3awb4.png" alt="enter image description here" /></a></p>
  
Tags: <wgs><indel><igv><chromosomes>
Title: Can I interpret 15x coverage area as a part of one strand is missing?
ThreadText: # 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
  
  
  ---
  
  ## 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.
  
  
  ---
  
  