Fixing low quality region

Ask questions about sequence improvement / finishing D. mojavensis projects here.
Post Reply
dpaetkau
Posts: 31
Joined: Fri Jun 05, 2009 6:18 pm

Fixing low quality region

Post by dpaetkau » Thu Aug 30, 2018 4:01 pm

As a refresher to the students projects, I was working on the DBIA2377019 project.

It has one low consensus quality region that looks like this:
Screen Shot 2018-08-30 at 11.55.13 AM.png
Screen Shot 2018-08-30 at 11.55.13 AM.png (120.5 KiB) Viewed 3393 times
There are many illumina reads to back up a claim that the correct sequence should be:
CCCT G AAAAAAAAAA CAAAAAT
rather than the sequence from read DBIA2377019
CCCT A GAAAAAAAAA CAAAAAT

The new sequence with the change would look like this:
Screen Shot 2018-08-30 at 11.55.13 AM.png
Screen Shot 2018-08-30 at 11.55.13 AM.png (120.5 KiB) Viewed 3393 times
So, is there enough evidence to make this change. Adding new sequences is not going to fix the problem as there are already many illumina reads added.

Thank you in advance for your help.
Don
Attachments
Screen Shot 2018-08-30 at 11.49.51 AM.png
Screen Shot 2018-08-30 at 11.49.51 AM.png (159.2 KiB) Viewed 3393 times

wleung
Posts: 185
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Fixing low quality region

Post by wleung » Fri Aug 31, 2018 3:19 pm

Yes. There is sufficient supporting data from the Illumina reads to change the consensus.

Post Reply