Mismatch correction using Illumina runs

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dpaetkau
Posts: 28
Joined: Fri Jun 05, 2009 6:18 pm

Mismatch correction using Illumina runs

Post by dpaetkau » Mon Nov 02, 2015 5:50 pm

Hello,

I would like to ask a question to be sure that we are finishing according to the current best practices.
I have a student that was wondering if the following logic is correct:
There was a HQD found at position 19117 on contig 1495012. It seems from the evidence of the Illumina reads that the consensus should not be changed. In order to correct the MNR, two base changes would also be needed to be made at positions 19117 and 19113. This does not seem to be a 454 mistake. It seems more likely that this is a sequence mapping error. Therefore, no changes were made.
A picture is enclosed to illustrate the area in question. Is her logic correct?
1495012.jpg
1495012.jpg (44.29 KiB) Viewed 3143 times

wleung
Posts: 179
Joined: Sun Feb 04, 2007 7:41 pm
Location: Washington University in St. Louis

Re: Mismatch correction using Illumina runs

Post by wleung » Thu Nov 05, 2015 9:07 pm

Yes. I agree with your assessment that the high quality discrepancies can likely be attributed to Illumina reads that have been misplaced and that the consensus should not be changed. The region contain multiple blue (transposon) tags so some of the Illumina reads that have been mapped to this region are likely to have been derived from other genomic copies of the transposon.

For documentation purposes, please add a comment tag to these types of regions with a brief note indicating that the discrepancies can likely be attributed to Illumina reads that have been misplaced.

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