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Table 4 Genomic relatedness calculated using Genome-to-Genome Distance Calculator

From: Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris

Query genome Reference genome Formula 1 (HSP length/total length) Formula 2 (identities/HSP length) Formula 3 (identities/total length)
  DDH Model C.I. Distance Prob. DDH ≥ 70 % DDH Model C.I. Distance Prob. DDH ≥ 70 % DDH Model C.I. Distance Prob. DDH ≥ 70 %
C. auris 6684 C. glabrata CBS 138 8.4 2.29 0.957 0 20.3 2.29 0.2049 0 9.7 2.29 0.9653 0
C. auris 6684 C. albicans SC5314 8.8 2.34 0.934 0 19.8 2.34 0.2107 0 10 2.34 0.9473 0
C. auris 6684 C. albicans WO-1 8.8 2.33 0.934 0 19.8 2.33 0.211 0 10 2.33 0.9478 0
C. auris 6684 C. lusitaniae ATCC 42720 10.4 2.48 0.856 0 19.2 2.48 0.2171 0 11.4 2.48 0.8866 0
C. auris 6684 S. cerevisiae S288c 8.4 2.29 0.958 0 20.4 2.29 0.2039 0 9.6 2.29 0.9667 0
  1. Distances are calculated by (i) comparing two genomes using the BLAT program to obtain HSPs/MUMs and (ii) inferring distances from the set of HSPs/MUMs using three distinct formulas. The distances are transformed to values analogous to DDH. The DDH estimate results from a generalized linear model (GLM) which also provides the estimate’s confidence interval (after the +/− sign). An additional bootstrap confidence interval is listed if this option was chosen in the job submission form. Logistic regression (with a special type of GLM) is used for reporting both the probabilities that DDH is > =70 % and > =79 %. GGDC is mainly used to calculate the in silico relatedness of the species