Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
how to best remove low-coverage reads horvathdp Bioinformatics 25 02-10-2015 09:15 AM
problem with low coverage genome sequencing wrch General 4 05-02-2014 10:56 AM
Low coverage sequencing, which strategy? Ole De novo discovery 3 02-29-2012 09:21 AM
Maq Ė how to filter low coverage areas? icg Bioinformatics 0 01-06-2011 12:49 AM
low 454 coverage combined with high solexa coverage strob Bioinformatics 7 10-07-2010 10:14 AM

Thread Tools
Old 09-28-2016, 07:57 PM   #1
Junior Member
Location: Sri Lanka

Join Date: Aug 2016
Posts: 6
Question Low coverage after alignment


I'm working with a illumina Miseq 2*300bp PE 8 sample library run on a single lane of a flowcell. Ref ~32Mbp in size. I aligned PE raw dataset for one sample against the reference sequence using BWA-mem and checked mapping statistics using Picard CollectAlignmentSummaryMetrics and CollectRawWgsMetrics. Some of the results are as below.

SD_COVERAGE 82.993179

output file from CollectAlignmentSummaryMetrics is also attached which shows that PCT_PF_READS_ALIGNED ~97% PF_HQ_ALIGNED_READS ~92% which I believe is good. But I'm confused with ~19% mean coverage. When I trim data I get a alignment with same quality but coverage is low as in the above case.

Can anybody give me any comments on this? Am I on the right track?

Attached Files
File Type: txt output_L2339.txt (2.3 KB, 5 views)
Rangika is offline   Reply With Quote

coverage, mapping statistics.

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:29 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO