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33 votes

Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

It is highly unlikely that there exist any protein that is made from completely identical nucleotide sequences across the entire human population. There will certainly be regions within a gene that ...
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23 votes
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Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

Humans have many variants There is variation. The project I use to help understand this natural variation is gnomAD. Using VarMap and a slightly out of date gnomAD file, I counted 16007805 protein-...
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8 votes

Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

At the whole-gene level, there is likely no absolute conservation of any human protein-coding gene at the population level, though there might be complete conservation between individuals. Keep in ...
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8 votes
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Are four-leaf clovers mutations, developmental errors, or something more complicated?

A recessive gene for four leaves has been identified (Tashiro et al., 2010). The clover is a tetraploid species and together with the fact that environmental conditions may also suppress the ...
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4 votes

Statistician confused about exact SNP data type

SNP is not a specific data type but rather a biological phenomenon. The abbreviation "Single Nucleotide Polymorphism" only means there is a variability (between individuals) in a single ...
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  • 562
4 votes

When does one decide to refer to a virus as a new variant?

We use them as synonyms. However, variant is, in my view, more colloquial than scientific. Strains are in the literature often defined by their distinct genome compared to other strains of the same ...
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  • 594
4 votes

What is the relationship between a "main" strain genome and its variant genome in archaea?

... I was reading the article about Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome in which they compare the Pyrococcus Furiosus reference ...
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3 votes
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CCTV cameras in Microbiology (Pathology) Laboratories

No - cameras would not capture the detail of the experiments being performed, nor would many of the experiments make sense without some context for the individual labels, if the camera could see them. ...
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  • 7,818
3 votes
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Do all tumour variants affect the disease pathway

Biology is complicated. It's hard to say without looking at the list of genes. Or indeed, even with the list of genes. What you are calling a "disease pathway" might instead just be a list ...
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3 votes

Online resource for downloading gene variant data?

Seems your variants are all possibly harmful mutations to human genes, in that case ClinVar can be quite useful, it returns hits to all your variants except L747_T751delinsP. I have never used the ...
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3 votes

Does zygosity have meaning for mitochondrial variants?

You abosolutely can have mixed populations of mitochondria in a cell (it is in fact very common). Therefore when you sequence the mtDNA you will get a completely variable percentace of reads ...
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  • 31
3 votes

What is a sequencing artifact?

Some specific artefacts are: apparent insertions or deletions in the sequence, which are really just skipped base or duplicated base errors during the sequencing apparent variants which do not exist ...
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3 votes
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What is a sequencing artifact?

Artifacts are variations introduced by non-biological processes. Sequencing involves a lot of chemical reactions, and changes in nucleotides that can seem like mutations are really introduced ...
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  • 149
2 votes

why and how multi allele gets reported during variant calling in vcf?

In your example the 4th column contains the reference allel on the given position. It is not said, that your sample has this. The 5th column contains all alternative alleles found on the given ...
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2 votes

What is a sequencing artifact?

I believe an artifact is something that appears in the first analysis but is not actually present in the sample. You would want to sort out all of the artifacts so that your final analysis is accurate....
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  • 19
2 votes
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Variant VCF: AD vs DP?

DP is the total number of read bases spanning a particular position. If you add up the different AD, you should get a number close to DP, the difference being merely in how the reads are filtered in ...
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  • 58
1 vote
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Statistician confused about exact SNP data type

I think the prevuious answers provide lots of valuable and relevant information, but let me add additional prospective: As noted, SNP is a single nucleotide polumorphism, whereas notation AA, Aa, aa, ...
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  • 3,772
1 vote

Is it true to say that the more an organism is smaller, the faster it's going through evolution?

I think that you are talking about what are sometimes called "rates of evolution", see also https://www.thenakedscientists.com/articles/questions/do-smaller-organisms-evolve-faster. That wiki is a ...
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1 vote
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Do these large spiders in Taiwan belong to different species?

The following is from Biogeography and Speciation Patterns of the Golden Orb Spider Genus Nephila (Araneae: Nephilidae) in Asia, Yong-Chao Su, Yung-Hau Chang, Deborah Smith, Ming-Sheng Zhu, Matjaž ...
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  • 5,087
1 vote

How to get phased haplotype from vcf file?

You should be able reformat BAM files to VCF files with PGDSpider. I find using specific softwares for this type data formatting tends to be error prone and not practical when having a large number ...
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  • 67.7k
1 vote

Definition of the different DNA regions

The Sequence Ontology project defines an intragenic variant as "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do ...
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  • 141
1 vote

Definition of the different DNA regions

We can take a look at the following picture (from wikipedia): The regions are then: intergenic: everything outside of the shown gene region <5 Kb downstream: outside of the transcribed region, ...
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  • 4,296
1 vote

What is this passage trying to say about Darwin's difficulty in explaining variation?

Remember this is all before the rediscovery of Mendel and the understanding of things like recessive traits and inheritance of discrete rather than blended traits. The problem is that, given an ...
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  • 36.7k
1 vote

Online resource for downloading gene variant data?

I think the correct nomenclature is EGFR L747_T751delinsP, based on http://varnomen.hgvs.org/recommendations/protein/variant/delins/ You can also use a translator tool like TransVar @smock2020 and @...
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1 vote

Online resource for downloading gene variant data?

You can use the Table Browser. For the variants, in the group field select variation, in the track field, select any database you are interested in, finally insert the genome position of your gene of ...
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  • 3,028

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