Answers.Body: <p>Black line represents an indel.  Read was lengthened to fit consensus.</p>
  <p>No black line (blank), no read/sequence.  Read likely ended or was truncated.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-25T14:52:23.320Z
Answers.Text: In general, this is true. However, for my dataset, these are all long reads which I know span the region I'm looking at. For some reason, the black lines (which should be there) are not present for some INDELs.
Answers.UserDisplayName: TimD1
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-24T13:31:26.837Z
Answers.LastActivityDate: 2021-05-24T13:31:26.837Z
Answers.UserDisplayName: Stuber
Body: <p><a href="https://i.sstatic.net/cdZ52.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cdZ52.png" alt="Integrated Genome Viewer image" /></a></p>
  <p>IGV (Integrated Genome Viewer) is a popular open-source tool for viewing alignment files. In my BAM file in IGV, some deletions have black lines running through them, and others don't. What causes this? Short black lines also appear adjacent to some mutations and insertions.</p>
  <p>I generated the CIGAR for the SAM file myself, and am wondering if I made an error. I didn't find anything in IGV's documentation about this.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-20T17:58:41.763Z
Comments.Text: What do you see when you hover over these black lines using your mouse? Hovering on a few deletions with/without the black lines might give you an idea on the differences between them.
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-20T19:39:31.740Z
Comments.Text: It doesn't show anything besides the general read metadata. Only insertions show the inserted bases on hover. Insertions with/without short black lines through them are indistinguishable on hover.
Comments.UserDisplayName: TimD1
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-24T16:18:30.733Z
Comments.Text: Those look like some single-T reads (i.e., reads with a single base). What do you see when you hover over them? Do you get a more coherent bit of info? What does the CIGAR look like for one of those?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-25T14:51:14.480Z
Comments.Text: They look like short reads, but it's actually a deletion within a long read that for some reason isn't showing a black line. I'm wondering what metadata difference in the SAM/BAM could possible cause the omission of the black line...
Comments.UserDisplayName: TimD1
Tags: <sam><igv><cigar>
Title: What does presence/absence of black lines mean in IGV?
ThreadText: # What does presence/absence of black lines mean in IGV?
  
  (Asked by: username_0 on 2021-05-20)
  
  [![Integrated Genome Viewer image](https://i.sstatic.net/cdZ52.png)](https://i.sstatic.net/cdZ52.png)
  
  IGV (Integrated Genome Viewer) is a popular open-source tool for viewing alignment files. In my BAM file in IGV, some deletions have black lines running through them, and others don't. What causes this? Short black lines also appear adjacent to some mutations and insertions.
  
  I generated the CIGAR for the SAM file myself, and am wondering if I made an error. I didn't find anything in IGV's documentation about this.
  
  **Tags:** sam, igv, cigar
  
  > **Comments:**
  > **username_1**: What do you see when you hover over these black lines using your mouse? Hovering on a few deletions with/without the black lines might give you an idea on the differences between them.  
  > **username_0**: It doesn't show anything besides the general read metadata. Only insertions show the inserted bases on hover. Insertions with/without short black lines through them are indistinguishable on hover.  
  > **username_2**: Those look like some single-T reads (i.e., reads with a single base). What do you see when you hover over them? Do you get a more coherent bit of info? What does the CIGAR look like for one of those?  
  > **username_0**: They look like short reads, but it's actually a deletion within a long read that for some reason isn't showing a black line. I'm wondering what metadata difference in the SAM/BAM could possible cause the omission of the black line...  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2021-05-24. Score: 1
  
  Black line represents an indel. Read was lengthened to fit consensus.
  
  No black line (blank), no read/sequence. Read likely ended or was truncated.
  
  > **Comments:**
  > **username_0**: In general, this is true. However, for my dataset, these are all long reads which I know span the region I'm looking at. For some reason, the black lines (which should be there) are not present for some INDELs.  
  
  ---
  
  