Table 4 Variants identified in relapse pairs

002

NS

146316

Rv0120c, fusA2

Translation

NS

345226

Rv0283, eccB3

Part of ESX-3 (essential, ESX-3 T7SS is implicated in metal homeostasis)

S

3135592

Rv2827c-109

INDEL (TC/TCC)

3600992

Rv3224B

Predicted membrane protein

006

S

1348678

Rv1205-41

S

1370403

Rv1227c

S

2828233

hisT down

010

NS

200390

Rv0170, mce1B

Part of ESX-1, essential for pathogenesis

012

NS

2510502

Rv2237A

CP, non-essential

017

INDEL (GC/GCC)

341124

Rv0281

Possible membrane protein

018

S

783720

fusA1

S

783729

fusA1

S

783732

fusA1

S

1476666

rrl

S

4050367

folE

019

NS

3884906

Rv3467

CHP, non-essential

024

S

848538

PPE12

025

S

1929374

Rv1703c

026

NS

1192723

Rv1069c

CP, non-essential

NS

1690758

Rv1499

CHP, non-essential

027

S

114494

nrp

031

S

175753

Rv0149

S

620981

Rv0530

S

1315992

pks4

NS

1540497

Rv1367c

CP, non-essential

S

2788333

plsB2

033

NS

3618159

Rv3240c, secA1

Protein export, essential

036

S

923816

lysT

NS

924229

Rvnt13, pheU

tRNA

NS

924234

Rvnt13, pheU

tRNA

S

924263

pheU

NS

1476973

Rvnr03, rrf

5S rRNA