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</> (less-/greater-than sign) denotes a reference skip. This occurs, for example, if a base in the reference genome is intronic and a read maps to two flanking exons. If quality scores are given in a sixth column, they refer to the quality of the read and not the specific base.
1. Introduce the reference of a SNP of interest, as an example: rs429358, in a database (dbSNP or other). 2. Find MAF/MinorAlleleCount link. MAF/MinorAlleleCount: C=0.1506/754 (1000 Genomes, where number of genomes sampled = N = 2504); [4] where C is the minor allele for that particular locus; 0.1506 is the frequency of the C allele (MAF), i.e. 15% within the 1000 Genomes database; and 754 is ...
Phred quality scores shown on a DNA sequence trace. A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing.
Permutational multivariate analysis of variance (PERMANOVA), [1] is a non-parametric multivariate statistical permutation test.PERMANOVA is used to compare groups of objects and test the null hypothesis that the centroids and dispersion of the groups as defined by measure space are equivalent for all groups.
N50 statistic defines assembly quality in terms of contiguity.Given a set of contigs, the N50 is defined as the sequence length of the shortest contig at 50% of the total assembly length.
An important part of the design of variant calling methods using NGS data is the DNA sequence used as a reference to which the NGS reads are aligned. In human genetics studies, high quality references are available, from sources such as the HapMap project , [ 10 ] which can substantially improve the accuracy of the variant calls made by variant ...
Ion Torrent sequencing: NGS technology based on the use of a semiconductor chip where the sample is loaded integrated with an ion-sensitive field-effect transistor able to sensitively detect reductions of the pH value due to the release of one or more protons after the incorporation of one or more dNTPs during sequencing by synthesis: the ...
Long-read aligners (e.g. minimap2 [35]) often support chimeric alignment and can be directly applied to long-read Hi-C data. Short-read Hi-C alignment is more challenging. Notably, Hi-C generates ligation junctions of varying sizes, but the exact position of the ligation site is not measured.