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Table 3 Table of sequence statistics for 16S, 18S, trnL, ITS, COI and COI-spun molecular datasets pooled across plots. Number of raw sequence reads, post-QC reads and their unique sequences, chimeras, OTUs at the 97 % threshold, α diversity, effective α diversity and number of phyla. The quality-control process included error correction of 454 sequence reads using Acacia [34]

From: Evaluating a multigene environmental DNA approach for biodiversity assessment

 

16S

18S

trnL

ITS

COI

COI-spun

Total

Raw reads

1,000,881

602,973

1,319,595

377,403

113,427

116,638

3,530,917

Post-QC reads

768,208

539,832

185,314

137,518

84,832

65,786

1,781,490

Post-QC unique sequences

337,849

150,121

105,377

50,166

51,737

25,708

720,958

Filtered reads

563,985

520,826

170,706

132,885

83,747

63,596

1,535,745

Filtered unique sequences

192,151

138,200

100,041

48,118

50,832

23,692

553,034

Chimeras +

147,652

12,130

5,554

2,110

1,013

2,094

170,553

OTUs

15,039

6,440

43,223

6,957

14,248

2,784

88,691 ∗∗

Singleton

8,427

2,419

26,537

3,848

6,056

1,497

48,784 ∗∗

α diversity

3,108.50

1,353.70

4,961.40

935.00

1,786.60

325.40

N/C ∗

Effective α diversity

295.22

69.48

1,293.63

77.77

631.77

17.23

N/C ∗

No. of phyla ++

43

58

49

35

60

31

109

  1. *N/C: not calculated
  2. **The total number of OTUs is just each number for each gene added together
  3. +The total number of unique sequences that were classified as chimeras by both USEARCH OTU clustering and UCHIME in UPARSE pipeline
  4. ++The number of phyla includes NCBI-defined phyla and equivalent high-level taxa