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Figure 7 shows the normalized reference tree distance (number of discordant reference tree bipartitions divided by the count of discordant and concordant reference tree bipartitions) for several combinations of tree size and number of edits, for inferred protein trees and the randomly permuted trees described earlier in "Benchmarking of EEEP" above.
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It excludes concordant homozygous reference calls.
NRD measures the proportion of differing genotypes between the WGA and genomic callsets, at sites called in both data sets, excluding concordant homozygous reference calls.
In particular, for heterozygous SNPs, the allele concordant with the reference is more likely to be mapped, resulting in a bias towards the reference allele and an inflated rate of false positive ASE.
NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing.
From the set of BAC clones that aligned concordant with the reference genome, 99.8% also aligned concordant with the AK1 assembly, with most of the discrepancies caused by phase differences (Supplementary Table 6).
A total of 107 well-characterized carbapenem resistant Enterobacteriaceae were evaluated and the results were 100% concordant with the reference test isolates.
Among the 170 TF genes for which we could construct a phylogenetic tree, 23 were inferred to be ORB+, of which 9 (39%) were recovered as topologically concordant with the reference.
The importance of accounting for within-gene transfer is even more-striking in the subset of protein-coding E. coli - Shigella gene sets that code for TFs, where almost 40% of ORB+ gene sets yield a protein tree concordant with the reference tree.
In each breed, roughly 0.1% of the mapping read pairs had no concordant alignment in the reference genome, referred to as discordant paired-end reads [ 2, 17], indicating a potential SV.
All of the obtained results are concordant with those of the reference method.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com