Kannapedia.net is getting a good face-lift.
Samples now have variant tables with annotation on their impact to the gene.
There is also an IGV integration. You need IGV installed locally but the Start|Jump links will open up you BAM file in IGV.
Samples now have variant tables with annotation on their impact to the gene.
There is also an IGV integration. You need IGV installed locally but the Start|Jump links will open up you BAM file in IGV.
You must have IGV open and then click the start link.
The sample's BAM will show up for viewing in IGV.
Once open, you can use the jump link to move swiftly around to each variant. This is a variant in THCAS.
The sample's BAM will show up for viewing in IGV.
Once open, you can use the jump link to move swiftly around to each variant. This is a variant in THCAS.
You can jump to other variants in the same gene. In this case we have one non-synonymous variant in phase with a synonymous variant in THCAS.
Cannabinoid synthase genes are cute but some folks can answer those questions with HPLC.
How about flowering genes?
This sample has a disruptive in frame deletion on a late flowering gene. And it's very rare in the population.
How about flowering genes?
This sample has a disruptive in frame deletion on a late flowering gene. And it's very rare in the population.
Looks to be heterozygous....
But its never this simple in cannabis.
Let's look at what other damaging variations it has.
But its never this simple in cannabis.
Let's look at what other damaging variations it has.
7 Damaging inframe deletions or insertions (indels) in Early and Late flowering genes.
When it comes to Indels, IGV can be very helpful to inspect the read frequency and if there appears to be any read mismapping with short reads. They all look real and diploid.
Here is another one in AAE1-2. This gene is involved in making the pre-cursors to cannabinoid synthesis.
It is not just a simple presence or absence of the cannabinoid synthase genes. One has to pay close attention to variants up stream in the pathway as well.
It is not just a simple presence or absence of the cannabinoid synthase genes. One has to pay close attention to variants up stream in the pathway as well.
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