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Sequence coverage (or depth) is the number of unique reads that include a given nucleotide in the reconstructed sequence. [1] [2] Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. [3] Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of ...
It can be thought of as the point of half of the mass of the distribution; the number of bases from all contigs longer than the N50 will be close to the number of bases from all contigs shorter than the N50. For example, consider 9 contigs with the lengths 2,3,4,5,6,7,8,9, and 10; their sum is 54, half of the sum is 27, and the size of the ...
From these numbers it is clear that the b + /b locus lies between the a + /a locus and the c + /c locus. There are 23 + 152 + 148 + 27 = 350 progeny showing recombination between genes A and B. And there are 81 + 23 + 27 + 89 = 220 progeny showing recombination between genes B and C.
The proportion of segregating sites within a gene is an important statistic in population genetics since it can be used to estimate mutation rate assuming no selection. For example it is used to calculate the Tajima's D neutral evolution statistic. A sequence alignment, produced by ClustalO, of mammalian histone proteins.
Further, there may be a bias in which certain codons are preferred in a gene, as a certain combination of codons may improve translational efficiency. [1] A 2022 study reported that synonymous mutations in representative yeast genes are mostly strongly non-neutral, which calls into question the assumptions underlying use of the K a /K s ratio.
A high coverage in shotgun sequencing is desired because it can overcome errors in base calling and assembly. The subject of DNA sequencing theory addresses the relationships of such quantities. Sometimes a distinction is made between sequence coverage and physical coverage. Sequence coverage is the average number of times a base is read (as ...
Gene dosage is the number of copies of a particular gene present in a genome. [1] Gene dosage is related to the amount of gene product (proteins or functional RNAs) the cell is able to express. Since a gene acts as a template, the number of templates in the cell contributes to the amount of gene product able to be produced.
These types of false-positive variants are filtered out by the duplex sequencing method since mutations need to be accurately matched in both strands of DNA to be validated as true mutations. Duplex sequencing can theoretically detect mutations with frequencies as low as 10 −8 compared to the 10 −2 rate of standard NGS methods. [1] [2] [10]
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