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Table 1 Detectable reads per sample and distribution by kingdom

From: Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples – a proof-of-principle assessment

Sample

Histological diagnosis

Total read pairs

Assigned read pairs

Unassigned read pairs

Eukaryotes excluding fungi

Fungi

Bacteria

Viruses

Archaea

1

Chromoblastomycosis

3,937,419

1,147,985

2,789,434

21,600

2046

478,980

645,351

8

2

Mucormycosis

9,624,603

3,993,184

5,631,419

1,826,409

4829

1,103,678

1,058,228

40

3

Histoplasmosis

10,377,343

9,642,335

735,008

8,649,198

1015

138,392

853,722

8

4

Mucormycosis

2,717,953

1,219,660

1,498,293

237,965

850

261,919

718,923

3

5

Histoplasmosis or cryptococcosis

6,697,156

2,829,244

3,867,912

841,420

3087

1,484,221

500,489

27

6

Chromoblastomycosis

6,986,916

5,321,271

1,665,645

416,898

995

3,399,811

1,503,362

205

7

Rhinosporidiosis

4,437,770

1,742,087

2,695,683

215,943

3209

826,178

696,741

16

8

Mycetoma

2,729,331

1,935,487

793,844

1,153,381

1661

125,046

655,398

1

9

Rhinosporidiosis

6,383,726

1,568,557

4,815,169

28,812

3579

906,363

629,763

40

10

Mycetoma

5,596,933

2,098,943

3,497,990

901,105

3678

627,175

566,972

13

11

Histoplasmosis

7,109,960

5,690,358

1,419,602

1,145,879

16,632

3,252,319

1,275,523

5

12

Histoplasmosis

3,083,524

1,148,615

1,934,909

205,871

6699

408,619

527,415

11

13

Chromoblastomycosis

12,529,855

6,557,056

5,972,799

4,427,985

8699

1,055,351

1,064,979

42

14

Histoplasmosis

7,901,861

6,886,130

1015,731

5,895,735

2171

413,407

574,811

6

15

Coccidioidomycosis

7,570,025

2,732,014

4,838,011

359,079

9784

1,757,949

605,165

37

16

Coccidioidomycosis

8,791,653

7,216,906

1,574,747

4,307,983

1696

2,422,677

484,421

129

17

Mycetoma

9,178,967

7,682,742

1,496,225

6,872,406

1116

237,152

572,064

4

18

Invasive amebiasis

16,947,754

15,543,806

1,403,948

583,362

561

13,508,300

1,447,733

3850

19

Invasive amebiasis

7,267,378

6,313,385

953,993

6,255,013

1446

45,602

11,324

0

20

Invasive amebiasis

22,840,836

22,215,617

625,219

21,555,613

2401

151,650

505,953

0

21

Invasive amebiasis

24,171,093

22,848,176

1,322,917

22,100,882

6631

193,348

547,309

6

22

Invasive amebiasis

29,225,435

28,785,110

440,325

28,194,606

1284

63,325

525,890

5

23

Invasive amebiasis

15,262,467

12,996,958

2,265,509

12,256,665

5047

138,208

597,018

20