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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