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Table 1 Comparision of different annotation

From: Improved Macaca fascicularis gene annotation reveals evolution of gene expression profiles in multiple tissues

Future

Human Gencode version 19

Refseq

NCBI 101 (2016.02)

Ensemble version1 (2017.12)

Computational annotation

Manual Annotation

Genes

57,820 (main chromosome without chrY)

-

33,368 (31,950 main chromosome without chrY)

28,592 (27,966 main chromosome without chrY)

23,282 (main chromosome without chrY)

13,413 (main chromosome without chrY)

Protein-coding genes

20,345

-

20,627

21,404

17,774

13,196

average length of genes

29,907 bp

-

41,827 bp

38,598 bp

43,579 bp

62,503 bp

transcripts

196,520

2037

76,559

53,156

27,029

-

average length of transcripts

34,243 bp

40,127 bp

80,039 bp

49,987 bp

44,243 bp

-

Number of transcripts per gene

3.4

1

2.29

1.86

1.16

-

CDSs

269,043

15,307

62,934

481,660

27,628

-

average length of CDSs

159 bp

147 bp

709 bp

155 bp

1410 bp

-

Exons

562,673

16,597

289,695

500,876

201,670

771,632

average length of exons

330 bp

217 bp

403 bp

218 bp

195 bp

615 bp

Number of exons per transcript

2.86

8.15

3.78

9.42

7.46

13.93

coverage rate(main chromosomes)

min

12.08%

1.08%(without chrY, chrM)

33.87%(without chrY)

27.45%(without chrY)

23.95%(without chrY, chrM)

18.14%(without chrY, chrM)

median

51.71%

3.07%(without chrY, chrM)

48.96%(without chrY)

39.94%(without chrY)

35.17%(without chrY, chrM)

29.96%(without chrY, chrM)

mean

51.17%

2.91%(without chrY, chrM)

48.14%(without chrY)

40.79%(without chrY)

35.92%(without chrY, chrM)

29.22%(without chrY, chrM)

max

92.50%

4.59%(without chrY, chrM)

68.36%(without chrY)

92.42%(without chrY)

50.57%(without chrY, chrM)

39.45%(without chrY, chrM)

coverage rate (genome, all main chromosomes)

 

50.39%

2.81%(without chrY, chrM)

46.8%(without chrY)

37.98%(without chrY)

33.94%(without chrY, chrM)

28.09%(without chrY, chrM)

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BMC Genomics

ISSN: 1471-2164

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