Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BWA mapping quality score is unstable

    Hi Everyone,

    Has anyone else noticed that the BWA mapping quality score is not deterministic so that if you map the exact same read/pair multiple times you sometimes get different mapping quality scores? This is not for pure repeats but for reads that have reasonable mapping quality scores around 30 and the read maps to the same position each time.

    I ran an experiment where I simulated 100 error-free paired-end reads from each position in dm3 chrM (read length=100, outer distance=300), and mapped them back to all of dm3 to compute the mapping quality score of each position. For about 1/3 of the starting positions, I would get 2 different mapping quality scores such that about half the reads at a position would have a mapping quality score of X and half the time it would get a score of X+7. For example the reads simulated starting at position 500 either get a mqs of 29 or 36.

    Does anyone have a good explanation for this? My understanding is the mapping quality score computation should be completely deterministic (except maybe if the pair distance is reestimated), but the results look like there is a random component - it is not always exactly 50-50 split between 2 values, but a tight distribution around 50-50.

    Thank you,

    Mike

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 09:45 AM
0 responses
201 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-03-2024, 08:54 AM
0 responses
211 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-02-2024, 03:00 PM
0 responses
193 views
0 likes
Last Post seqadmin  
Working...
X