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Structural distance between wild-type and mutant sequences was calculated from base pairing probability matrices (Sabarinathan et al. 2013).
The structural distance (d max ) between wild-type and mutant sequences was calculated from base pairing probability matrices [ 33].
We then multiply the probabilities calculated from base genotypes, allelic phase information, and allele frequencies, rescale (to ensure all posteriors sum to 1), and output the posterior probability for each HLA allele pair.
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Equations 1a through 1d show that Bulmer-equilibrium parameters can be calculated from base-generation parameters using simple equations.
Subsequently, variance of the most frequent base in that position is calculated from the base composition.
It is calculated from buffer base offsets by assuming a mean extracellular haemoglobin concentration of 50 g/l.
The expected accuracy can then be calculated from the base pair reliabilities by (5) The consensus structure with the maximal reliability is then calculated using a Nussinov-style algorithm [ 30], where the base pairs are evaluated with reliabilities.
However, the difference between these two measures of reliability can be predicted using the equilibrium reliabilities calculated from the base PEV reliabilities and the proportions selected among males and females [ 16].
Agreement between unmeasured anions calculated from the base deficit (BDUMA) and Stewart Fencl methods (strong ion gap) was assessed by linear regression with the use of the ordinary least-squares method (Microsoft Excel).
For many organisms, the dispersion is greater when calculated from data based on week of report, than when calculated from data based on week of specimen (Technical Appendix Figure 4, right panel).
For each platform, the mean coverage depth over each exon was calculated from the base-resolved coverage depth integrated over the exon length, considering only aligned bases with high-quality mapping (Q ≥20) and base-quality (Q ≥20) scores.
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