Answers.Body: <p>Yes, this is a low complexity region.</p>
  
  <p>Regions are considered low complexity (or having a simple sequence) when they contain an abundance of a single base, or an abundance of short tandem repeats. The simplest is a tandem repeat of a single base (e.g. <code>AAAAAAAAAAAAAAAA</code>), also called a homopolymer. In your case there is a 3-unit tandem repeat of <code>TAAAAA</code>, and surrounding As (with a few intermingled Ts). Depending on the genetic history of this region, it might be that those other As and Ts are derived from the same <code>TAAAAA</code> unit, with some slipping that has occurred during replication to create a cryptic (i.e. non-perfect) repeat structure.</p>
  
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Answers.CreationDate: 2018-01-09T07:54:54.347Z
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Answers.UserDisplayName: gringer
Answers.Body: <p>Yes, that's a short low complexity region wedged between a SINE and an snRNA. More importantly, your alignments have MAPQ of 0 (that's why they're filled with white in IGV), which will happen if they map equally well to multiple locations. Without looking at the sequence one can use that alone to determine that these are not trustworthy mappings.</p>
  
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Answers.Text: Oh, I didn’t know about white meaning MAPQ=0. Very useful!
Answers.UserDisplayName: Konrad Rudolph
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Answers.UserDisplayName: Devon Ryan
Body: <p>I have a screenshot where many of my reads were aligned to a region that I <strong>suspect</strong> a low complexity region. Although you can't see, all those reads are <strong>clipped</strong> in the cigar strings. Sample cigar strings: <em>64S32M29S, 74S32M18S</em> etc... Consequently, the actual sequence mapped to the genome is <strong>less</strong> than the read length.</p>
  
  <p>I have a feeling that my alignments are bogus because of the complexity and clipping, but I'm not sure if the complexity is indeed low. All I see is a few "T" between a bunch of "A". How to define a low complexity region?</p>
  
  <p><strong>Q:</strong> Is this a low complexity region in the human hg38 genome? Would that be fair if I report "<em>the alignments are likely be errors due to the low complexity and alignment clipping</em>"? </p>
  
  <p><a href="https://i.sstatic.net/fJC2X.png" rel="noreferrer"><img src="https://i.sstatic.net/fJC2X.png" alt="enter image description here"></a></p>
  
Tags: <genome>
Title: Is this a low complexity region in our human genome?
ThreadText: # Is this a low complexity region in our human genome?
  
  (Asked by: username_0 on 2018-01-09)
  
  I have a screenshot where many of my reads were aligned to a region that I **suspect** a low complexity region. Although you can't see, all those reads are **clipped** in the cigar strings. Sample cigar strings: *64S32M29S, 74S32M18S* etc... Consequently, the actual sequence mapped to the genome is **less** than the read length.
  
  I have a feeling that my alignments are bogus because of the complexity and clipping, but I'm not sure if the complexity is indeed low. All I see is a few "T" between a bunch of "A". How to define a low complexity region?
  
  **Q:** Is this a low complexity region in the human hg38 genome? Would that be fair if I report "*the alignments are likely be errors due to the low complexity and alignment clipping*"?
  
  [![enter image description here](https://i.sstatic.net/fJC2X.png)](https://i.sstatic.net/fJC2X.png)
  
  **Tags:** genome
  
  
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  ## 2 answers
  
  ### Answer by username_2 on 2018-01-09. Score: 7 | Accepted answer
  
  Yes, that's a short low complexity region wedged between a SINE and an snRNA. More importantly, your alignments have MAPQ of 0 (that's why they're filled with white in IGV), which will happen if they map equally well to multiple locations. Without looking at the sequence one can use that alone to determine that these are not trustworthy mappings.
  
  > **Comments:**
  > **username_3**: Oh, I didn’t know about white meaning MAPQ=0. Very useful!  
  
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  ### Answer by username_1 on 2018-01-09. Score: 6
  
  Yes, this is a low complexity region.
  
  Regions are considered low complexity (or having a simple sequence) when they contain an abundance of a single base, or an abundance of short tandem repeats. The simplest is a tandem repeat of a single base (e.g. `AAAAAAAAAAAAAAAA`), also called a homopolymer. In your case there is a 3-unit tandem repeat of `TAAAAA`, and surrounding As (with a few intermingled Ts). Depending on the genetic history of this region, it might be that those other As and Ts are derived from the same `TAAAAA` unit, with some slipping that has occurred during replication to create a cryptic (i.e. non-perfect) repeat structure.
  
  
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