Answers.Body: <blockquote>
    <p>This is, for two identical samples with identical final coverage, sample A having an average insert size of 250bp and sample B having an average of 450bp, would the fraction of MAPQ=0 change between the two?</p>
  </blockquote>
  
  <p>For human, I <em>expect</em> sample B will have fewer MAPQ=0 reads (I don't have concrete data to prove). A large part of human genome consists of ALU repeats. The average size of an ALU is ~320bp. If your insert size is ~450bp, you can map reads into most of isolated ALUs in principle. With ~250bp insert, fragments in the middle of ALUs won't be mappable uniquely.</p>
  
  <p>Note that to see the difference, you need to use a mapper that sufficiently takes the advantage of paired-end information.</p>
  
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Answers.Text: Does bwamem take advantage of it?
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Answers.Body: <p>Yes, as a general rule of thumb mappability increases with insert size (up to a limit) and read length. Whether this will actually occur in a given case will depend more on how randomly the sequencing samples from the genome to begin with (i.e., if the library prep happens to select for/against high mappability regions then the insert size won't much matter). The basic reason behind this is that if one end of a read aligns to a repetitive element that the likelihood of being able to use the other end as an anchor will increase a bit if it's further away. Now having said that, Illumina sequencers in particular like a certain fragment length for efficient sequencing, so you can't go too crazy on increasing the insert sizes and still get decent output (unless you modify your library prep).</p>
  
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Body: <p>When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, does the percentage of the non-N fraction of the human genome as MAPQ=0 depend on the insert sizes of the genomic fragments?</p>
  
  <p>This is, for two identical samples with identical final coverage, sample A having an average insert size of 250bp and sample B having an average of 450bp, would the fraction of MAPQ=0 change between the two?</p>
  
Tags: <sam><illumina><mapq>
Title: Does the MAPQ=0 fraction of a BAM file depend on the insert sizes?
ThreadText: # Does the MAPQ=0 fraction of a BAM file depend on the insert sizes?
  
  (Asked by: username_0 on 2018-01-09)
  
  When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, does the percentage of the non-N fraction of the human genome as MAPQ=0 depend on the insert sizes of the genomic fragments?
  
  This is, for two identical samples with identical final coverage, sample A having an average insert size of 250bp and sample B having an average of 450bp, would the fraction of MAPQ=0 change between the two?
  
  **Tags:** sam, illumina, mapq
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2018-01-09. Score: 4 | Accepted answer
  
  Yes, as a general rule of thumb mappability increases with insert size (up to a limit) and read length. Whether this will actually occur in a given case will depend more on how randomly the sequencing samples from the genome to begin with (i.e., if the library prep happens to select for/against high mappability regions then the insert size won't much matter). The basic reason behind this is that if one end of a read aligns to a repetitive element that the likelihood of being able to use the other end as an anchor will increase a bit if it's further away. Now having said that, Illumina sequencers in particular like a certain fragment length for efficient sequencing, so you can't go too crazy on increasing the insert sizes and still get decent output (unless you modify your library prep).
  
  
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  ### Answer by username_1 on 2018-01-11. Score: 0
  
  > This is, for two identical samples with identical final coverage, sample A having an average insert size of 250bp and sample B having an average of 450bp, would the fraction of MAPQ=0 change between the two?
  
  For human, I *expect* sample B will have fewer MAPQ=0 reads (I don't have concrete data to prove). A large part of human genome consists of ALU repeats. The average size of an ALU is ~320bp. If your insert size is ~450bp, you can map reads into most of isolated ALUs in principle. With ~250bp insert, fragments in the middle of ALUs won't be mappable uniquely.
  
  Note that to see the difference, you need to use a mapper that sufficiently takes the advantage of paired-end information.
  
  > **Comments:**
  > **username_0**: Does bwamem take advantage of it?  
  
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