Using the Bowtie2 read aligner [ 13] with the default settings we were able to align between 82.0 % and 96.2 % of sequenced reads as concordant pairs to the final genome assemblies, indicating that the genome assemblies are relatively complete.
We added to the number of conditions categorized as concordant and discordant, and validated concordance and discordance categorizations done in previous work (Table 3).
The cases were all negative or positive in the three assays, or positive in pathological diagnosis, nested PCR but negative in IHC representing the coincidental cases with a concordance percentage of 84% (147/175), while others were not as concordant (Table 3).
The combined rates of concordance including alleles ambiguously typed by SBT but resolved by MIT-NGS as concordant for all four HLA loci between the two methods was 98.3%.
Imaging findings were characterized as concordant when there was agreement in positive detection with both tracers, and as discordant in cases of discrepancy between the two tracers' uptake.
Isolates that shared the same spoligotype pattern except for one of 43 spacers, were also classified as concordant genotypes.
Some of the morphological features in this lineage (e.g., the absence of a nucleus with permanently condensed chromosomes in the trophont stage) have, accordingly, been interpreted as concordant evidence for a sister relationship between Noctiluca and dinokaryotes [31] [33].
However, when varying the distance calculations, e.g. not calculating Euclidean distances and/or not using logarithmic probe intensity values, the clustering results of the two technologies were not as concordant (data not shown).
GEE performs case-control comparisons in family data by accounting for correlations among related individuals such as concordant and discordant siblings, relative pairs, as well as including unrelated close contacts.
When the isolate of an index case and the isolate of a diseased contact from the same household shared the same spoligotype pattern (genotype), these were referred to as concordant genotypes.
Half of the volunteers from these two sites were drawn from large prospective studies of long-term, stable sexually active couples of HIV discordant status (the volunteer's partner was HIV positive), and half were drawn from couples identified during couples' VCT as concordant HIV-negative (both partners HIV uninfected).
