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These three indices for rare and common variants on each autosome were shown in Additional file 2 (bias, MSE) and Additional file 3 (type I error rate).
Using SNPnexus, we were able to assess in details the functional consequences of these variants on each isoform from RefSeq, Ensembl, Vega, AceView and UCSC.
To further explore this phenomenon, the reference genome was divided into 4,256 disjoint intervals of length 100 kb and we counted the amount of heterozygous and homozygous variants on each interval (see Methods).
The chromosomal forms definition does not allow the unambiguous assignment of all possible karyotypes, either because of technical difficulties with scoring inversion haplotypes (the phase of variants on each chromatid), or because they are by definition 'recombinants' or otherwise segregating in multiple chromosomal forms (e.g. the 'FOREST' karyotypes that are shared between MOPTI and SAVANNA).
Generally, haplotypes are comprised of allelic variants on each of the two chromosomes at the same locus, though the definition and utilization varies in application from linking multiple polymorphisms across several loci down to multiple polymorphisms in a single gene [ 23].
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Finally, given that one of the two strands can be the one that exhibits a characteristic pattern, we train a predictive model on both variants of each repeat sequence: one obtained from the forward strand and the other from the complementary reverse strand.
Zinc crystallites laid on each other in a specific variant on each grain of electropolished surfaces, but stacked zinc crystallites were seen in variants all over the substrate on mechanically polished substrates.
Definitive determination of the extinction coefficients would require analytical analysis of the enzymatic products for each P450 variant on each substrate, which is beyond the scope of this study.
New binary variables were generated, in both Lima and Durban datasets, as follows: (i) for each allelic variant on each of the three HLA loci (HLA-A, HLA-B, and HLA-C) a binary variable was created with value 1 if the subject had that respective variant and 0 otherwise; (ii) for each OLP a binary variable was set with value 1 if the subject has responded to this OLP and 0 otherwise.
Typical aggregation curves and standard curves can be found in Figure 5 figure supplement 2. Quantification was carried out as follows: to measure the relative activity of Spy variants on α LA, each Spy variants were used at three ratios in duplicate (Spy: α LA ratios = 0.1, 0.15, and 0.2) in the aggregation assay.
First, the brown alga Feldmannia sp. is able to produce viruses having genomes with two different sizes and two variants of each, depending on the temperature at which the algae are cultivated [ 40].
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