Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Bueller_007
    started a topic Odd characters in samtools mpileup output

    Odd characters in samtools mpileup output

    I'm struggling to figure out what some of the characters in my samtools mpileup output are. Here's one of the offending bases (scaffold1:25513). There are many.

    Code:
    scaffold1       25513   G       20      <<,,,,,a,A,aa,a,AA..    #A.CCFG6G6F67E:F<6GF
    So it tells me that the read depth is 20, and this is confirmed by counting the number of characters in each of the last two columns. But I have absolutely no idea what the "<" character represents in the read_bases column (column #5).

    The only special characters I'm expecting to see are '.' and ',' (indicating forward and reverse matches) '+' and '-' (indicating indels), and '^' (followed by a symbol indicating read-mapping quality) and '$' (indicating the beginning and end of a read respectively).

    So can anyone tell me what '<' means in column 5?


    EDIT: To answer my own question somewhat, '<' and '>' indicate a "reference skip" according to the mpileup documentation. (Although they are not mentioned in the pileup format documentation, which is why I couldn't find them.) However, I have absolutely no idea what "reference skip" means, so I'm still out of luck. If it's referring to a base that is not covered (e.g. due to splicing) then shouldn't the coverage ideally be reported as 18, not 20?
    Last edited by Bueller_007; 08-26-2011, 04:52 PM.

Latest Articles

Collapse

  • seqadmin
    Recent Developments in Metagenomics
    by seqadmin





    Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
    09-23-2024, 06:35 AM
  • seqadmin
    Understanding Genetic Influence on Infectious Disease
    by seqadmin




    During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.

    Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...
    09-09-2024, 10:59 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 10-02-2024, 04:51 AM
0 responses
8 views
0 likes
Last Post seqadmin  
Started by seqadmin, 10-01-2024, 07:10 AM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 09-30-2024, 08:33 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 09-26-2024, 12:57 PM
0 responses
16 views
0 likes
Last Post seqadmin  
Working...
X