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The number of SNPs and error rate more strongly influence pool proportion inference, where read count contributes little.
In this meta-analysis, postoperative morbidity occurred in 68 of 299 patients for a pool proportion of 23%95%5% CI 18.5-21.8).
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In Figure 5, bottom, we present the phylogenies and pool proportions inferred by the lineage model.
Errors encountered most often took the form of merged lineages or "migrating" pool proportions and nearest-neighbor interchanges between taxa.
Across 13 samples amplified in triplicate, pool proportionality was maintained within similar values across all samples and libraries, with standard deviations of pool proportions less than 3%.
The inferred model appears to recapitulate much of the relative location of these branches on the phylogenetic tree and also reflect appropriate pool proportions.
Summing over the lineages at each position combines the pool proportions and the SNP state to give the expected reference allele frequency for pool i and SNP j: p ij = ∑ k = 1 K s ik ⋅ (1 − l kj ).
The strengths of this systematic review include explicit eligibility criteria, conduct of a comprehensive search and the usage of random-effects model to pool proportions in keeping with the large heterogeneity.
The pie charts of pool proportions below the inferred trees show the 5%, mean, and 95% estimates with colors shaded from darkest for the 5% estimates through the lightest for the 95% estimates.
We note that pool proportions of the unknown sample (green in Figure 6) indicate that it likely has a similar collection location to that of the 12-m sample.
Direct comparison of simulated pool proportions for lineages 2 and 3 appears to indicate poor performance, although we observe that combining the simulated values for these lineages (in blue) substantially improves the agreement.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com