Table 2 The presence or absence of mutations in CRISPR-associated genes in Mycobacterium tuberculosis complex strains compared to reference template H37Rv NC_000962.3 4411532 bp. The mutations are listed in ascending order of their location relative to the reference H37Rv chromosome

deletion

cas2

3123625

Beijing RD207 & all deleted-CRISPR strains

Rv2816c

deletion

cas1

3123967

Beijing RD207 & all deleted-CRISPR strains

Rv2817c

SNP

cas1

3124014

cga/cgc

Ser/S->Ala/A

T3_Eth defining

Rv2817c

SNP

cas1

3124352

gct/gat

Ser/S->Ile/I

T3_Eth defining

Rv2817c

SNP

cas1

3124743

cac/caa

Val/V->Leu/L

proto-Beijing defining

Rv2817c

deletion

csm6

3124996

Beijing RD207 & deleted-DR A (Haarlem)

Rv2818c

SSP

csm6

3125070

T3_Eth specific

Rv2818c

SSP&SNPs

csm6

3125120

proto-Beijing specific

Rv2818c

SNP

csm6

3125171

gtt/gct

Asn/N- > Ser/S

ERR212132 specific

Rv2818c

SSP

csm6

3125690

ERR212132 specific

Rv2818c

SNP

csm6

3125235

ttg/tta

Gln/Q- > stop

BCG specific

Rv2818c

deletion

csm5

3126240

Beijing RD207

Rv2819c

SNP

csm5

3126279

atc/att

Asp/d- > Asn/N

SRR671740 specific

Rv2819c

SNP

csm5

3127273

gtg/gtt

His/H- > Asn/N

proto-Beijing defining

Rv2819c

SNP

csm4

3127466

tcg/gcg

Arg/R- > Arg/R

BCG specific

Rv2820c

SNP

csm4

3127717

tgt/tgc

Thr/T- > Ala/A

T3_Eth defining

Rv2820c

truncation

csm4

3127930

Beijing RD207 truncation

Rv2820c

SNP

csm4

3127931

ttt/att

Lys/K- > Asn/N

Beijing-defining

Rv2820c

None^a

csm3

Rv2821c

None^a

csm2

Rv2822c

SNP

cas10/csm1

3129359

tcc/tct

Gly/G- > Arg/R

CDC1551 specific

Rv2823c

SNP

cas10/csm1

3129675

gcg/gtg

Arg/R- > His/H

C_0253-12 and C_0309-12 specific

Rv2823c

SNP

cas10/csm1

3130682

gcc/acc

Gly/G- > Gly/G

F11 specific

Rv2823c

SNP

cas10/csm1

3131188

gag/gaa

Leu/L- > Phe/F

Beijing BT2 specific

Rv2823c

SSPs & SNPs

cas10/csm1

3131470

Found in all MTBC strains

Rv2823c

None^a

cas6

Rv2824c