SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
[general question]gatk, dindel, IGV sirmark Bioinformatics 10 03-13-2013 06:44 AM
General question about NGS Nepher General 0 01-02-2013 01:33 AM
informatics/general question mzpitman Bioinformatics 0 03-05-2012 06:31 PM
General question about TopHat mhayes Bioinformatics 1 02-03-2012 02:00 PM
general genetics question hoffmann General 3 10-14-2010 01:38 AM

Reply
 
Thread Tools
Old 12-22-2016, 03:38 AM   #1
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 349
Default General IGV question about pileup

In IGV what does a variant found only in white space denote. I don't think its real but trying to figure it out. For example, in the attached all the C are located in the white space. Thank you .
Attached Images
File Type: png IGV_Image.png (11.9 KB, 8 views)
cmccabe is offline   Reply With Quote
Old 12-22-2016, 05:24 AM   #2
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,204
Default

I'm not sure because the fill can be set via preferences to denote various characteristics of the read. But it is attractive to think that it might denote in this case a failure to map the paired read? Attractive because that would suggest that the locus has a paralog elsewhere in the genome with a slightly different sequence.

--
Phillip
pmiguel is offline   Reply With Quote
Reply

Tags
igv

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 06:40 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO