Supplementary Table 1. Retained sequence reads for

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Supplementary Table 1. Retained sequence reads for

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Tremellomycetes. Saccharomycetes. Eurotiomycetes. Dothideomycetes. Supplementary Table 1. Retained sequence reads for individual mock community ...

Supplementary Table 1. Retained sequence reads for individual mock community isolates based on merged paired-end reads processing vs. the bioinformatics pipeline used in this study (forward reads only)* Sequence reads (merged pipeline)** ITS1

Dothideomycetes

ITS1

ITS2

89341

114073

9

7

265551

205917

41053

15088

Cladosporium sphaeospermum

54967

21013

3

9

90956

83206

26587

31306

Aspergillus brasiliensis

2378

8384

10

95

124246

118078

27452

32185

Aspergillus flavus

3230

28976

32

9

122954

119969

43221

20589

Aspergillus niger Exophiala spinifera Penicillium chrysogenum

Ascomycota

Trichophyton mentagrophytes Candida albicans Candida glabrata

Saccharomycetes

Candida parapsilosis

SSU

Sequence reads (forward reads only)**

Alternaria alternata

Aspergillus fumigatus

Eurotiomycetes

ITS2

LSU

SSU

LSU

23

15445

24

5

79575

70330

49896

21851

2809

13602

9

8

126611

58681

48695

18224

18529

60048

7

33

41316

105446

42554

21076

1671

52857

5

10

235040

136974

20113

37680

31

41651

4

30

177433

124798

19897

19945

184891

31017

20

22

218982

48410

47027

28812

58

18510

8

21

39969

26062

37351

11366

139502

76934

16

5

167202

106998

38019

34513

Candida tropicalis

89415

71195

9

7

107748

101414

26691

34239

Yarrowia lipolytica

141177

155283

24

26

5308

173674

23499

23947

Saccharomyces cerevisiae

58104

52629

1

35

96085

65569

14141

34961

Sordariomycetes

Fusarium solani

16579

14

3

2

71390

148863

34640

27017

Tremellomycetes

Cryptococcus neoformans

74547

36599

16

7

85571

53422

33871

22269

150989

65057

4

21

150269

83533

25508

31947 28938

Basidiomycota

Trichosporon dermatis Malassezia furfur

Exobasidiomycetes

9401

9

9

17

16395

30689

41570

Malassezia globosa

31529

17893

6

24

46780

36685

31304

21620

Malassezia pachydermatis

16674

7

4

8

27286

43115

22967

35618

*Merged reads processing was via the same bioinformatics pipeline as that used in this study, with the following alterations: primer binding regions were trimmed and forward and reverse reads were merged (via fastq_mergepairs in usearch), and all single-read-specific processing was omitted (incl. trimming read tails, and trimming any retained reverse primer binding regions and associated junk sequence) . **Sequence read counts are after all filtering, immediately prior to even depth subsampling