Table 1. Tennessee clade statistics and details for all isolates and individual clades, including number of isolates, hqSNP analyses details and statistics (reference genome used, mean hqSNP distance and range, and mean percent reads mapped and range), core and accessory genes as determined by Roary (Page et al., 2015), and loci associated with inclusion in each clade as determined by Scoary (Brynildsrud et al., 2016).
| Clade | No. Isolates | hqSNP Analysis | Core Genome (genes) | Accessory Genome (genes) | No. of Locia Significantly Associated with Inclusion [No. genes] | No. of Significant Positively Associated Locia[No. genes] | |||
|---|---|---|---|---|---|---|---|---|---|
| Reference | Avg hqSNP distance [range] | Reads Mapped (%) [range] | |||||||
| analyzed together | analyzed separately | ||||||||
| All Isolates | 111 | GCF_000341425.1 | 645.3 [0-1427] | – | 96.14 [90.44-98.44] | 4,022 | 3,920 | – | – |
| SRS2420927 | 627.5 [0-1416] | – | 96.91 [90.35-99.70] | ||||||
| SRS2822480 | 631.6 [0-1404] | – | 95.92 [90.35-99.77] | ||||||
| SRS3010019 | 630.2 [0-1429] | – | 97.59 [89.55-99.85] | ||||||
| I | 54 | GCF_000341425.1 | 118.8 [0-605] | 119.8 [0-618] | 96.33 [90.44-98.38] | 4,106 | 2,513 | 153 [338] | 54 [94] |
| SRS2420927 | 114 [0-594] | 119.4 [0-631] | 97.72 [90.35-99.70] | ||||||
| II | 4 | GCF_000341425.1 | 193.8 [3-362] | 210.3 [3-396] | 97.60 [96.73-98.44] | 4,290 | 322 | 22 [221] | 16 [207] |
| SRS2822480 | 189.7 [2-353] | 197.5 [2-369] | 99.48 [98.77-99.77] | ||||||
| III | 48 | GCF_000341425.1 | 63.2 [1-366] | 65.1 [0-376] | 95.96 [91.41-97.65] | 4,115 | 889 | 155 [332] | 101 [238] |
| SRS3010019 | 64.3 [0-367] | 66.0 [0-361] | 98.99 [94.19-99.85] | ||||||
Notes.
a
Each locus is a single gene or group of multiple genes.