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. 2016 Jun 30;7:985. doi: 10.3389/fmicb.2016.00985

Table 3.

Comparison of common vs. outbreak-specific reference intergenic SNPs.

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
a

This study/short reads in NCBI = A, WGS = B, assembled genomes in NCBI = C.

b

F = mixed analysis with reads missing for some strains.