Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Samtools Flagstat, what is "with itself and mate mapped" mean?

    Here is my flagstat output after running bwa mem on my paired end data.

    25730940 + 0 in total (QC-passed reads + QC-failed reads)
    111474 + 0 secondary
    0 + 0 supplementary
    0 + 0 duplicates
    25300974 + 0 mapped (98.33% : N/A)
    25619466 + 0 paired in sequencing
    12809733 + 0 read1
    12809733 + 0 read2
    24045298 + 0 properly paired (93.86% : N/A)
    25182938 + 0 with itself and mate mapped
    6562 + 0 singletons (0.03% : N/A)
    1071166 + 0 with mate mapped to a different chr
    297377 + 0 with mate mapped to a different chr (mapQ>=5)


    So from my understanding, 93.86% of my reads are properly paired which means the read and its mate mapped with decent distance to the same chromosome. So does "with itself and mate mapped" simply mean that both reads did map but maybe not all of them are within good distance from each other? Does it also mean both did map to the same chromosome? It is unclear to me what that category means but it does make sense to me that the number of reads would be higher.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
9 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
49 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
67 views
0 likes
Last Post seqadmin  
Working...
X