Questions tagged [variant]
The variant tag has no usage guidance.
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Additional to SNP (variant) calling, what is genotype calling in human genome?
Variant calling in human genome aims to determine in which positions there is polymorphic site or in which positions at least one of the dna bases differs from a human reference genome. Then beside ...
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CCTV cameras in Microbiology (Pathology) Laboratories
Isn't it highly beneficial to have CCTV cameras installed in all Microbiology Labs in the COVID-19 times?
As the COVID vaccines are already developed, the research & development carried further in ...
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Do all tumour variants affect the disease pathway
I have analysed some lung tumour samples for somatic variants which generated a list of genes affected by those variants. I tried to analyse KEGG pathways to see what could they disrupt. However, many ...
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What is the relationship between a "main" strain genome and its variant genome in archaea?
I am going to analyze DNA sequencing data in order to try to extrapolate some information about the survival strategy of Pyrococcus Furiosus to gamma irradiation, as maybe you already know from all ...
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Statistician confused about exact SNP data type
I'm from a statistical (not biological) background, and I'm very confused about what exactly is the "data" associated with a SNP. Below, I'll explain things as best I can--please correct me ...
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When does one decide to refer to a virus as a new variant?
I've read that SARS-Cov-2 has several variants, e.g.:
Can the U.S. keep Covid variants in check? Here's what it takes.
Novavax’s Vaccine Works Well — Except on Variant First Found in South Africa
...
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Is it true to say that the more an organism is smaller, the faster it's going through evolution?
As someone who never formally learned biology, I assume that currently;
The number of species of (non Archaea) Bacteria
The number of species of Algae
The number of species of Plankton
The number of ...
user22497
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Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?
All humans have the same sort of proteins in our bodies. Take haemoglobin for example.
Is the gene coding for haemoglobin in my body identical to everyone else's gene or is there slight variations ...
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What is a sequencing artifact?
I'm rather new to bioinformatics, so this might be a rather basic question, but what are sequencing artifacts, in the context of variant calling?
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Do these large spiders in Taiwan belong to different species?
I see both of these spiders (and others) frequently on hiking trips outside of Taipei. Their large webs are often high overhead between trees but can be right across a hiking trail that hasn't been ...
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why and how multi allele gets reported during variant calling in vcf?
This might be a very basic question for many here. With the basic understanding of inheritance, eventhough there is a possibility of multiple genotypes due to multi alleles, the resulting genotype can ...
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The concept of high genetic load of disease and non-random segregation of deleterious variants
I'm new in this field. I was reading Shakeel et al. (2018) and came across the below sentences
The rate of emergence and distribution of deleterious variants in populations is important in ...
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How to get phased haplotype from vcf file?
Although I'm reading all days and nights, still confused in this area. I have hundreds of BAM files (from whole-genome sequencing of a given human population). I was wondering how I can obtain phased ...
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Definition of the different DNA regions
Reading from Oshima et al. (2016):
We identified 3,868 noncoding mutations including 394 located <5 Kb downstream, 1,762 intergenic, 1,621 intronic, 81 <5 Kb upstream, 7 UTR 3′, 2 UTR 5′, and ...
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What is this passage trying to say about Darwin's difficulty in explaining variation?
This passage, from the book "How humans evolved" by Robert Boyd, says that one of the problems Darwin had at the time was that he struggled to convincingly explain how variation could be maintained; ...
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Online resource for downloading gene variant data?
I have a long list of gene variations. For example, Here are 4 of them:
CBL Q249E
TERT H412Y
SF3B1 R625H
EGFR L747_T751delinsP
The first term identifies the gene, the second identifies the ...
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What are the exact reason causing missing calls in a VCF file from exome sequencing?
My data is a VCF file from exome sequencing variant call. I'm not very familiar with the sequencing process and variant calling process. I noticed that there are some missing genotypes, which is ...
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Is a novel homozygous SNV reasonable?
I'm doing some variant discovery in a human trio (affected child, non-affected mother, non-affected father) and I have found what looks like a homozygous novel mutation. All of the aligned reads in ...
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Are VCF headers supposed to change over time?
VCF headers describing the content of the INFO field are supposed to give additional information about a variant.
Example. A VCF file can be annotated against ...
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Use of pipe character in VCF info field
While annotating my VCF file with ClinVar, I noted the following value for the CLNSIG field (i.e., clinical significance):
...
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Are four-leaf clovers mutations, developmental errors, or something more complicated?
What causes about 1 in 10,000 clovers to have four instead of three leaves? Will progeny(?) grown from its flower's seeds have a higher probability than that of also having four leaves?
From the ...
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Does zygosity have meaning for mitochondrial variants?
I am working on a system that annotates variants in human DNA sequences. One of the pieces of information reported is the zygosity of the variant. I noticed that mitochondrial variants are also shown ...
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Variant VCF: AD vs DP?
In my VCF file from GATK, I have the following definitions for AD and DP.
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