Questions tagged [variant]

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What does an allele frequency of 0 mean in gnomAD v3?

There is a single nucleotide variant: 18-47394-G-A (GRCh38) with an allele count and allele frequency of 0. As I understand it, this means that there are no alleles in the population with this variant,...
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1answer
34 views

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 ...
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4answers
4k views

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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3answers
959 views

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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69 views

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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0answers
31 views

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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3answers
289 views

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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3answers
317 views

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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1answer
68 views

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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78 views

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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0answers
32 views

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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71 views

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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38 views

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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103 views

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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1answer
862 views

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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1answer
368 views

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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1answer
1k views

Variant VCF: AD vs DP?

In my VCF file from GATK, I have the following definitions for AD and DP. ...