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Table 2 Completeness and contamination for 31 ICoVeR-refined genome bins for AD microbiome dataset

From: ICoVeR – an interactive visualization tool for verification and refinement of metagenomic bins

Bina

Marker lineageb

Metagen. abund. %c

GC %

ICoVeR

MyCC

MetaBAT_1

MetaBAT_2

CONCOCT

Compl. %

Cont. %

Compl. %

Cont. %

Compl. %

Cont. %

Compl. %

Cont. %

Compl. %

Cont. %

1

Bacteria (UID2495)

22.3

36.1

98.9

0

98.9

0

98.9

0

98.9

0

100.0

18.8

2

Bacteroidales (UID2654)

6.3

41.7

96.6

0.4

98.9

39.2

96.6

0.4

96.6

2.2

100.0

82.3

3

Clostridiales (UID1212)

1.6

41.9

95.3

1.3

96.6

1.8

95.0

0.7

74.8

0.7

98.0

1.7

4

Firmicutes (UID241)

2.6

58.8

94.9

2.0

94.9

2.2

90.3

2.0

90.3

2.0

98.3

6.0

5

Bacteria (UID209)

1.5

42.0

94.8

1.7

94.8

3.7

90.8

0

90.8

0

94.8

2.0

6

Euryarchaeota (UID54)

1.5

59.9

92.2

0.2

94.7

4.7

85.8

0.1

85.8

0.1

94.6

42.8

7

Bacteria (UID2495)

1.1

51.9

66.7

0.0

94.7

51.0

66.7

0

66.7

0

100.0

101.7

8

Bacteria (UID2569)

8.8

46.7

82.91

2.5

93.4

23.8

75.6

7.7

75.7

9.8

100.0

99.4

9

Bacteria (UID209)

0.7

51.9

92.8

3.2

92.8

1.5

80.0

0.6

80.0

0.6

92.7

3.2

10

Bacteria (UID209)

1.0

51.1

92.2

0

91.4

1.7

93.6

6.8

93.6

6.8

98.2

19.1

11

Bacteroidetes (UID2605)

1.2

46.6

85.9

3.8

90.4

22.0

58.2

2.2

67.1

6.1

88.0

3.8

12

Firmicutes (UID239)

2.4

55.3

89.8

2.7

90.1

6.8

85.2

3.2

85.2

3.2

100

72.2

13

Bacteria (UID2495)

1.1

51.1

87.3

2.2

87.3

3.8

76.3

0

76.8

0

96.5

92.0

14

Bacteria (UID2495)

0.8

53.3

83.8

0.6

84.9

7.6

66.4

0.4

66.3

0.4

94.6

42.8

15

Bacteria (UID2570)

12.0

41.6

81.6

2.5

84.3

5.3

73.7

0.5

74.8

1.1

100.0

99.4

16

Firmicutes (UID1022)

0.7

54.2

63.9

2.0

83.4

17.2

48.0

0.2

43.8

0.2

100.0

72.2

17

Bacteroidetes (UID2605)

1.2

45.3

91.2

0.6

82.0

14.1

91.0

1.1

91.2

1.6

96.5

54.0

18

Bacteria (UID2495)

0.6

46.1

76.3

3.8

78.5

7.2

48.6

0

48.6

0

100

82.3

19

Bacteria (UID2982)

1.4

58.4

77.3

5.3

77.7

5.3

56.2

1.4

56.2

1.4

77.7

2.6

20

Firmicutes (UID241)

0.5

50.7

60.4

2.1

77.6

8.7

62.9

9.8

63.4

18.5

99.8

110.8

21

Bacteria (UID2565)

0.6

50.9

65.5

1.1

66.6

1.7

25.5

1.1

25.5

1.1

67.6

12.2

22

Clostridiales (UID1212)

0.3

45.4

62.01

2.4

63.7

4.0

NB

NB

63.0

5.1

23

Thermoanaerobacterales (UID1420)

0.6

35.8

51.8

3.2

63.7

7.3

28.9

0.1

29.0

0

51.8

3.2

24

Bacteria (UID209)

0.4

32.4

66.8

3.6

63.3

3.6

14.9

0

16.7

0

72.7

24.2

25

Bacteroidetes (UID2605)

0.5

49.9

59.0

1.0

60.0

5.0

46.2

0.7

46.2

0.7

75.5

3.01

26

Bacteria (UID2570)

0.3

49.6

51.3

3.3

56.8

10.2

NB

NB

96.6

54.0

27

Firmicutes (UID241)

0.3

52.3

49.5

1.0

56.8

6.0

12.8

0

NB

47.0

1.1

28

Bacteria (UID2569)

0.6

49.7

54.5

2.1

54.5

2.1

11.2

0

NB

62.4

15.3

29d

Clostridiales (UID1120)

0.1

47.4

14.6

0.7

53.7

8.1

NB

NB

45.2

3.8

30

Bacteroidetes (UID2605)

3.4

52.3

99.5

0.5

52.4

0.7

98.6

0.5

93.3

0.5

100.0

101.7

31

Bacteria (UID2495)

1.7

52.7

95.6

0.1

49.4

0

78.0

0.1

93.4

0.1

96.6

91.9

  1. MetaBAT_1 - ‘sensitive/specific’ mode
  2. MetaBAT_2 - ‘superspecific’ mode
  3. aNumber corresponds to the ICoVeR-refined bin (Table S2)
  4. bMarker lineage was defined by CheckM
  5. cMetagenomic abundance corresponds to the % of reads mapping to the contigs binned inside each bin
  6. dBased on the wide range in the GC content, the pattern of contigs abundances across the multiple samples and the level of contamination, we judged this bin to be a mixture of several low abundant organisms. Therefore, the ICoVeR-refined genome bin was less complete than the corresponding MyCC and CONCOCT genome bins
  7. Completeness and contamination were calculated with CheckM (highlighted in bold font for ICoVeR-refined bins). NB – no genome bin assigned