Table 3.
Isolate | Sequences analyzeda | SNPs in isolates, in intergenic regions | Commentsb | ||
---|---|---|---|---|---|
Compared to reference EC4115 | Compared to outbreak strain | ||||
FS | B103 | A | 1 | 1 | Reference specific allele |
B104 | A | 0 | 1 | ||
B105 | A | 0 | Reference | ||
B106 | A | 0 | 1 | ||
B107 | A | 0 | 1 | ||
BG | B112 | A | 0 | 0 | |
B113 | A | 0 | 0 | ||
B114 | A | 0 | Reference | ||
TB | EC4401 | B | 1 | Reference | F |
EC4402 | A | 0 | 27 | ||
EC4436 | A | 40 | Excluded | ||
EC4437 | A | 40 | Excluded | ||
EC4439 | A | 5 | Excluded | ||
EC4448 | A | 0 | 27 | ||
EC4486 | B | 3 | 31 | ||
TJ | EC4501 | B | 8 | 16 | F |
TW14588 | C | 1 | Reference | ||
CD | EC1738 | B | 67 | Excluded | F |
EC1734 | B | 0 | 4 | ||
EC1735 | A | 0 | 0 | ||
EC1736 | A | 0 | Reference | ||
EC1737 | A | 0 | 0 | ||
TP | EC1863 | A | 2 | Reference | High diversity |
EC1864 | A | 1 | 5 | ||
EC1866 | A | 2 | 6 | ||
EC1868 | A | 2 | 5 | ||
EC1869 | A | 10 | 14 | ||
EC1870 | A | 6 | 11 | ||
FF | EC1845 | A | 0 | 1 | Reference specific allele |
EC1846 | A | 0 | 1 | ||
EC1847 | A | 0 | 1 | ||
EC1848 | A | 0 | 1 | ||
EC1849 | A | 0 | 1 | ||
EC1850 | A | 0 | 1 | ||
EC1856 | A | 0 | Reference | ||
EC1862 | A | 0 | 1 |
This study/short reads in NCBI = A, WGS = B, assembled genomes in NCBI = C.
F = mixed analysis with reads missing for some strains.