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Table 2 Result summary of ITS data analyses (Clustering step)

From: CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

 

No error allowed

Two base pair error allowed

A NALYSIS I 1

95%

96%

97%

98%

99%

95%

96%

97%

98%

99%

TCB:TCC

12:12

13:14

14:15

17:18

29:41

14:15

15:17

16:20

19:27

41:68

TSB:TSC

4:3

4:4

5:5

5:4

13:14

4:5

4:4

4:6

5:6

24:27

B LAST ANALYSIS 2

          

TBHB:TBHC

5:6

6: 8

7: 8

8:9

16:20

6:7

7:9

8:11

9:15

24:39

TUBHB:TUBHC

5:6

6:8

7:8

8:8

11:11

6:7

7:8

8:10

9:10

12:12

ESB:ESC

4:5

5:6

6:6

7:8

11:15

4:5

5:7

6:7

7:11

8:24

UESB:UESC

4:5

5:6

6:6

7:7

8:9

4:5

5:6

6:6

7:8

8:9

OSB:OSC

1:1

1:2

1:2

1:1

8:5

2:2

2:2

2:4

2:4

16:15

UOSB:UOSC

1:1

1:2

1:2

1:1

5:4

2:2

2:2

2:4

2:3

6:5

A NALYSIS II 2

          

TCB:TCC

40:70

42:86

45:102

58:177

133:385

42:74

44:86

47:106

61:188

140:408

TSB:TSC

13:22

13:26

14:31

26:67

98:198

14:25

14:30

15:31

28:68

104:208

B LAST ANALYSIS 2

          

TBHB:TBHC

25:52

27:59

29:75

36:133

88:304

26:55

28:63

30:78

37:141

92:322

TUBHB:TUBHC

25:32

27:35

29:36

32:40

41:45

26:34

28:37

30:37

33:42

42:46

ESB:ESC

16:41

18:41

20:52

21:81

22:148

17:37

19:43

21:55

22:91

23:155

UESB:UESC

16:24

18:24

20:26

21:27

22:32

17:23

19:25

21:27

22:30

23:34

OSB:OSC

9:18

9:18

9:23

15:52

66:156

9:18

9:20

15:23

69:50

69:167

UOSB:UOSC

9:15

9:15

9:15

15:22

29:30

9:15

9:16

15:15

29:23

29:30

  1. Table providing statistics about the clustering steps run on the example dataset. Both BLASTCLUST and CD-HIT were used for clustering the unique sequences (with zero or two mismatches in the forward primer) at 95%, 96%, 97%, 98%, and 99% sequence identity and 50% sequence coverage. The table also summarizes the statistics of BLAST-based evaluation method of clusters.
  2. Subscript B and C means results from BLASTCLUST and CD-HIT respectively.
  3. 1TC (Total Cluster) is the number of clusters obtained at sequence identity 95%, 96%, 97%, 98%, and 99% irrespective of number of sequences in each cluster, TS (Total singletons) is the number of cluster with single sequence.
  4. 2TBH (Total BLAST Hit) is the number of OTUs obtained; TUBH (Total Unique BLAST Hit) is the number of unique BLAST hits obtained from the TBH, ES (Excluding Singletons) is the number of BLAST hits excluding clusters with single sequence (singletons) only; UES is the unique number of BLAST hits obtained from ES; OS (Only Singletons) is the number of BLAST hits obtained from singletons; UOS is the unique number of BLAST hits obtained from OS.
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BMC Bioinformatics

ISSN: 1471-2105

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