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Table 1 Isolate characteristics: DST and data derived from WGS including mapping indicators

From: Unraveling Mycobacterium tuberculosis genomic diversity and evolution in Lisbon, Portugal, a highly drug resistant setting

Isolate

DSTa

SCG

PGG

Spoligotypeb

SNPs

INDELsc

Mapping Indicatorsd

 

First-Line

Second-Line

  

SIT

Clade

Non-synonymous mutations (Ns)

Synonymous mutations (S)

Total in Coding Regions (Tc)

Total in Non-Coding Regions

Total

Ns/S Ratio

Tv/TsRatio

Tc/Total

Total

Size Range

Mean Read Depth

Coverage (%)

ARS10348

IRS

ETH

5

2

20

LAM1

410

296

706

243

949

1.3851

0.5865

0.7439

96

1-24

135.18

98.86

ARS11131

IRSP

CAP AMK OFX MOX ETH

5

2

1106

LAM4

381

286

667

237

904

1.3322

0.6308

0.7378

95

1-24

101.56

98.89

ARS11285

IRS

AMK OFX MOX

4

2

119

X1

429

302

731

283

1014

1.4205

0.6031

0.7209

114

1-37

159.38

99.83

ARS11463

I

nd

5

2

64

LAM6

382

255

637

241

878

1.4980

0.5575

0.7255

76

1-24

52.42

99.47

ARS11661

IS

nd

5

2

1106

LAM4

378

284

662

234

896

1.3310

0.6443

0.7388

96

1-24

110.16

98.84

ARS12740

IRSP

ETH

5

2

1106

LAM4

392

287

679

239

918

1.3659

0.6456

0.7397

95

1-24

97.66

98.81

ARS1717

IRP

OFX ETH

6a

3

2258

Unknown

263

158

421

160

581

1.6646

0.5651

0.7246

67

1-27

68.89

99.76

ARS1760

I

nd

5

2

64

LAM6

379

262

641

242

883

1.4466

0.5725

0.7259

83

1-53

69.23

99.40

ARS1900

IRSEP

CAP KAN OFX ETH

5

2

20

LAM1

414

301

715

250

965

1.3754

0.6009

0.7409

101

1-24

148.85

98.75

ARS1930

IRSP

na

5

2

42

LAM9

389

268

657

228

885

1.4515

0.6158

0.7424

90

1-52

90.43

98.81

ARS2061

IRP

CAP AMK KAN OFX ETH CS PAS

5

2

1106

LAM4

379

283

662

239

901

1.3392

0.6346

0.7347

89

1-24

80.51

98.83

ARS2202

IRSP

OFX ETH CS

5

2

20

LAM1

404

284

688

243

931

1.4225

0.5889

0.7390

91

1-24

79.46

98.99

ARS2573

I

nd

5

2

20

LAM1

400

277

677

231

908

1.4440

0.6250

0.7456

97

1-49

82.71

99.03

ARS3649

IRSEP

KAN OFX ETH

5

2

20

LAM1

399

282

681

242

923

1.4149

0.5814

0.7378

91

1-24

72.67

98.92

ARS3806

I

nd

5

2

2535

Unknown

386

283

669

233

902

1.3640

0.6277

0.7417

85

1-24

195.56

98.84

ARS4857

IRP

na

5

2

1106

LAM4

381

279

660

234

894

1.3656

0.6418

0.7383

92

1-24

91.12

98.86

ARS5858

IREP

OFX

5

2

20

LAM1

395

284

679

243

922

1.3908

0.6401

0.7364

102

1-24

142.10

98.98

ARS6483

IRSEP

OFX ETH

5

2

20

LAM1

406

303

709

246

955

1.3399

0.5839

0.7424

98

1-24

92.22

98.79

ARS6539

IS

nd

5

2

20

LAM1

407

303

710

249

959

1.3432

0.5933

0.7404

63

1-24

273.98

98.87

ARS6559

I

nd

5

2

81

LAM9

394

292

686

233

919

1.3493

0.5953

0.7465

86

1-24

63.55

98.76

ARS7496

IS

nd

2

1

1

Beijing

589

410

999

405

1404

1.4366

0.6404

0.7115

175

1-39

109.62

99.30

ARS7571

I

nd

5

2

211

LAM3

388

265

653

244

897

1.4642

0.5749

0.7280

93

1-24

123.02

99.48

ARS7860

IS

nd

5

2

811

LAM4

378

279

657

232

889

1.3548

0.6318

0.7390

86

1-24

72.59

98.60

ARS7884

IRSEP

OFX ETH

5

2

20

LAM1

409

300

709

244

953

1.3633

0.5874

0.7440

100

1-24

177.31

98.81

ARS8437

IRSP

CAP ETH

5

2

20

LAM1

405

296

701

247

948

1.3682

0.6005

0.7395

92

1-24

179.07

98.78

ARS8600

I

nd

5

2

20

LAM1

407

291

698

238

936

1.3986

0.6262

0.7457

74

1-49

254.44

98.97

ARS9427

I

nd

3a

1

26

CAS1-Delhi

632

411

1043

422

1465

1.5377

0.5773

0.7119

152

1-36

44.07

99.82

FF181_97

IRS

na

5

2

20

LAM1

417

300

717

249

966

1.3900

0.6185

0.7422

24

1-9

772.29

98.99

FF291_98

IRS

na

5

2

20

LAM1

416

294

710

250

960

1.4150

0.6063

0.7396

31

1-18

658.49

98.97

FF359_98

IRS

na

5

2

20

LAM1

419

293

712

254

966

1.4300

0.5946

0.7371

31

1-18

836.93

99.01

FF674_96

Susceptible

na

4

2

91

X3

428

323

751

276

1027

1.3251

0.6047

0.7313

34

1-33

961.69

99.76

HCC1095_10

IRE

nd

3b

2

53

T1

429

314

743

292

1035

1.3662

0.5577

0.7179

119

1-24

185.45

99.61

HCC1276_11

IRSEP

CAP AMK OFX MOX ETH

5

2

1106

LAM4

392

281

673

243

916

1.3950

0.6350

0.7347

96

1-24

159.36

98.81

HCC1470_11

IRSEP

CAP AMK KAN OFX MOX ETH CS PAS

5

2

20

LAM1

412

295

707

251

958

1.3966

0.5830

0.7380

99

1-24

96.90

98.76

HCC759_09

IR

ETH

2

1

1

Beijing

623

414

1037

418

1455

1.5048

0.6102

0.7127

160

1-28

70.73

99.39

HCC916_10

IRSEP

CAP AMK KAN OFX ETH

5

2

1106

LAM4

373

281

654

238

892

1.3274

0.6044

0.7332

103

1-24

145.85

98.82

HPV105_09

S

nd

5

2

1752

LAM1

400

281

681

244

925

1.4235

0.6214

0.7362

37

1-22

591.50

98.93

HPV113_08

IRSEP

ETH

6a

3

54

MANU2

222

126

348

140

488

1.7619

0.5945

0.7131

62

1-24

167.28

99.94

HPV115_08

IRSEP

CAP AMK KAN OFX ETH

5

2

1106

LAM4

312

225

537

196

733

1.3867

0.7318

0.7326

76

1-21

179.43

98.82

HPV157_06

IS

nd

5

2

17

LAM2

397

287

684

248

932

1.3833

0.5760

0.7339

90

1-24

96.25

98.87

HPV50_09

Susceptible

nd

5

2

20

LAM1

397

291

688

238

926

1.3643

0.6554

0.7430

69

1-24

281.12

98.94

HPV51_09

Susceptible

nd

3c

2

137

X2

420

309

729

276

1005

1.3592

0.5677

0.7254

29

1-18

632.88

99.60

HPV65_08

Susceptible

nd

6a

3

Unknown

Unknown

247

160

407

162

569

1.5438

0.5837

0.7153

15

1-18

1149.11

99.57

HPV70_09

Susceptible

nd

5

2

1803

LAM1

380

277

657

224

881

1.3718

0.6343

0.7457

26

1-45

1410.21

99.65

HVNG1

IRSEP

CAP AMK KAN

5

2

20

LAM1

308

225

533

201

734

1.3689

0.7082

0.7262

76

1-24

154.30

98.78

IHMT134_09

IRSP

RFB ETH

5

2

20

LAM1

332

228

560

203

763

1.4561

0.6935

0.7339

83

1-24

171.49

98.77

IHMT149_09

IRSEP

RFB CAP AMK OFX MOX ETH

5

2

1106

LAM4

313

226

539

193

732

1.3850

0.6849

0.7363

75

1-21

168.54

98.81

IHMT194_11

IRSEP

RFB CAP AMK ETH

5

2

1106

LAM4

382

274

656

236

892

1.3942

0.6318

0.7354

83

1-24

47.61

98.96

IHMT288_95

IRSP

RFB ETH

5

2

20

LAM1

415

304

719

247

966

1.3651

0.6230

0.7443

98

1-24

197.48

98.84

IHMT295_08

IRSEP

RFB ETH

2

1

1

Beijing

528

337

865

358

1223

1.5668

0.7284

0.7073

127

1-59

181.48

99.18

IHMT308_08

IRP

RFB ETH

5

2

1106

LAM4

334

228

562

201

763

1.4649

0.7524

0.7366

76

1-21

205.47

98.79

IHMT359_03

R

nd

5

2

Orphan

LAM1

406

289

695

247

942

1.4048

0.6276

0.7378

31

1-22

727.91

98.93

IHMT361_08

IREP

CAP ETH

5

2

1106

LAM4

305

232

537

193

730

1.3147

0.6278

0.7356

70

1-24

191.20

98.80

IHMT69_11

IRSEP

RFB CAP AMK ETH

2

1

1

Beijing

609

420

1029

415

1444

1.4500

0.6307

0.7126

169

1-39

202.92

99.36

IHMT80_11

IRSEP

RFB CAP AMK ETH

5

2

1106

LAM4

380

277

657

236

893

1.3718

0.6318

0.7357

87

1-24

63.98

98.95

IHMT82_09

IRS

RFB CAP ETH

5

2

20

LAM1

313

221

534

190

724

1.4163

0.6808

0.7376

81

1-24

121.47

98.69

  1. aFirst-Line: I - Isoniazid, R - Rifampicin, S - Streptomycin, E - Ethambutol, P - Pyrazinamide; Second-Line: ETH - Ethionamide, KAN - Kanamycin, AMK - Amikacin, OFX - Ofloxacin, MOX - Moxifloxacin, RFB - Rifabutin, PAS - Para-amino salicylic acid, CS - Cycloserine.
  2. bSpoligotype inferred from SpolPred software (Coll et al., [89]).
  3. cSmall INDELs called by SAMtools from mapping to M. tuberculosis H37Rv.
  4. dRelative to M. tuberculosis H37Rv.
  5. na, Not available.
  6. nd, Not done.
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