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Table 4. Nucleotide content and gene count levels of the metagenomes

From: Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron

 

SG only Metagenome

SG + Fe Metagenome

 

Number

% of Total

Number

% of Total

DNA, total number of bases

152,660,070

100.00%

154,120,208

100.00%

DNA coding number of bases

130,438,005

85.44%

136,080,382

88.29%

DNA G+C number of bases

62,858,797

41.18%*

70,930,796

46.02%*

DNA scaffolds

57,147

100.00%

65,160

100.00%

CRISPR Count

51

 

4

 

Genes total number

197,271

100.00%

193,491

100.00%

Protein coding genes

195,006

98.85%

192,751

99.62%

RNA genes

2,265

1.15%

740

0.38%

rRNA genes

294

0.15%

16

0.01%

5S rRNA

106

0.05%

9

0.00%

16S rRNA

75

0.04%

3

0.00%

18S rRNA

1

0.00%

4

0.00%

tRNA genes

1,971

1.00%

724

0.37%

Protein coding genes with function prediction

127,406

64.58%

129,389

66.87%

without function prediction

67,600

34.27%

63,362

32.75%

not connected to SwissProt Protein Product

195,006

98.85%

192,751

99.62%

Protein coding genes with enzymes

33,383

16.92%

30,632

15.83%

w/o enzymes but with candidate KO based enzymes

26,793

13.58%

32,919

17.01%

Protein coding genes connected to KEGG pathways3

37,533

19.03%

34,348

17.75%

not connected to KEGG pathways

157,473

79.83%

15,8403

81.87%

Protein coding genes connected to KEGG Orthology (KO)

63,949

32.42%

57,111

29.52%

not connected to KEGG Orthology (KO)

131,057

66.44%

135,640

70.10%

Protein coding genes connected to MetaCyc pathways

32,243

16.34%

29,552

15.27%

not connected to MetaCyc pathways

162,763

82.51%

163,199

84.34%

Protein coding genes with COGs3

121,020

61.35%

123,077

63.61%

with Pfam3

115,645

58.62%

118,589

61.29%

with TIGRfam3

33,743

17.10%

33,969

17.56%

in internal clusters

77,655

39.36%

73,856

38.17%

Protein coding genes coding signal peptides

48,556

24.61%

49,644

25.66%

Protein coding genes coding transmembrane proteins

43,693

22.15%

43,726

22.60%

COG clusters

4,125

84.65%

3,974

81.55%

KOG clusters

0

0.00%

0

0.00%

Pfam clusters

4,447

37.33%

4,293

36.04%

TIGRfam clusters

2,580

64.13%

2,489

61.87%

  1. * GC percentage shown as count of G’s and C’s divided by a total number of G’s, C’s, A’s, and T’s. This is not necessarily synonymous with the total number of bases.