In IGV is this a heterogeneous mutation or false call?
2
0
Entering edit mode
4 weeks ago
Tuck898 • 0

Hi all,

I'm hoping someone might be able to enlighten me on if this could be a true heterogeneous mutation. The count is 22% so a little higher to rule out it not being. How would I go about more investigation to confirm if this mutation is a positive? The read quality are roughly QV 37 average, some 39. I would be interested for any advice. Thanks in advance!

percentage

read quality

collapsed view

mutations IGV heterogeneous • 704 views
ADD COMMENT
0
Entering edit mode

I've just displayed clipped bases and this is what it shows. Does this look right?

enter image description here

enter image description here

enter image description here

ADD REPLY
0
Entering edit mode
4 weeks ago

there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP at this place.

ADD COMMENT
0
Entering edit mode

Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I check if there is a DUP by displaying the clipped bases please? thanks!

ADD REPLY
0
Entering edit mode

Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out?

enter image description here

enter image description here

ADD REPLY
0
Entering edit mode

yeah.. look at that, there is something wrong in your alignment, many reads were mapped in a location but they are all clipped, so something in 5'/3' is not related to the mapped sequence. Forget about your SNP.

how would I check if there is a DUP by displaying the clipped bases please

look at a clipped sequences, blat it, you might find the location upstream/downstream of the current location

ADD REPLY
0
Entering edit mode

Thanks for that! I'll try and have a look and see what is amiss if I can... In your opinion what do you feel is wrong in my alignment from what you can see? I guess the SNP is insignificant :D

Still learning so thanks for all the input.

ADD REPLY
0
Entering edit mode

When click the blat it brings me to chr19 and mentions the RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sound stupid but does this make sense to what I've previously showed about the clipped bases. Image below to where blat sequence took me. many thanks!

enter image description here

ADD REPLY
0
Entering edit mode

RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sound stupid but does this make sense to what I've previously showed about the clipped bases

it's too hard to answer without having a look at the data. It could be a rearrangement between the locus of both genes.

ADD REPLY
0
Entering edit mode

No worries, I can completely appreciate that. I am having investigations similar to a condition causes by the RYR2 gene and was wondering if what I am showing you could be a possible cause or not (and if I am wasting my time looking at this region). Is there anything else I can do to double check this exon? thanks again :)

ADD REPLY
0
Entering edit mode
4 weeks ago

Since all the reads that show the alternate allele have to be clipped to align there, I'd say those reads are misaligned. I would say that is not a true SNP.

ADD COMMENT
0
Entering edit mode

Thanks for the input :)

ADD REPLY

Login before adding your answer.

Traffic: 1356 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6