Table 2 Summary of variants confirmed using Sanger sequencing post whole genome sequencing

1

CV_0436

acrR

G179T^a

SNP

R60L

456,438 - > 457,085, 648 bp/215 AA

Transcription repressor of multidrug efflux pump

G375GAT^a

INS

Premature termination, 141 AA

acrAB operon, TetR (AcrR) family

2

CV_4365

marC

C4648G

SNP

No Change

708,719 - > 4,709,366

multiple drug resistance protein

3

CV_4191

rpsL

G117T^b

SNP

R86S

4,519,516 < − 4,519,887, 372 bp/123 AA

30S ribosomal protein S12

4

CV_3410

pabC

A147deletion^b

DEL

Premature termination, 226 AA

3,703,561 < − 3,704,373, 813 bp/270 AA

4-amino-4-deoxychorismate lyase

5

CV_1596

kdpD

G167deletion^b

DEL

Premature termination, 682 AA

1,719,330 < − 1,722,017, 2688 bp/895 AA

2 component regulatory protein sensor kinase. Osmosensitive K+ channel histidine kinase KdpD (EC 2.7.3.)

6

CV_0066

CV_0066

G655C^c

SNP

P219A

75,121 < − 76,422, 1302 bp/433 AA

Hypothetical protein

7

Nt CDS

nt cds

1263524^c

SNP

between CV_1197 and tRNA Ser

Cv_1197 - polysaccharide/polyol phosphate ABC transporter ATPase

8

CV_0464

CV_0464

A4273C^c

G4274A^c

T4276A^c

C4277G^c

G4278C^c

C4344G^c

SNP

SNP

SNP

SNP

SNP

SNP

Synonymous

478,148 - > 483,712, 5565 bp/1854 AA

Hypothetical protein, Homologous to Fibronectin type III domain protein