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Table 1 Comparison of direct and indirect pairwise coordinate translations for the 12- Drosophila dataset

From: A universal genomic coordinate translator for comparative genomics

Source

Target

Total blocks

Direct mapped

% of Tot mapped

Melanogaster Star Configuration

Sechellia Star Configuration

Clade center configuration

Mapped

Ident. (%)

Mapped

Ident. (%)

Mapped

Ident. (%)

D.ana

D.ere

52808

23003

43%

22923

99.0

22744

98.3

22923

99.0

 

D.gri

53157

7889

16%

8498

96.3

7775

89.9

8083

93.5

 

D.moj

53000

8316

16%

8362

95.9

7648

88.1

8122

93.2

 

D.sim

53012

21720

41%

21975

98.7

21766

98.2

21975

98.7

 

D.wil

53435

8011

16%

8048

92.8

8056

93.1

7424

86.2

 

D.yak

53375

23168

43%

23065

98.3

22898

98.7

23065

98.3

D.ere

D.gri

61131

9121

16%

9536

96.9

8743

90.6

8607

87.5

 

D.moj

60856

9341

15%

9238

96.9

8395

87.3

8373

85.9

 

D.per

60645

16423

27%

16288

98.0

16296

97.0

15898

95.3

 

D.pse

61162

17539

28%

17459

98.6

17337

97.2

17115

96.0

 

D.sim

61335

46231

76%

46011

98.4

45936

98.3

46011

98.4

 

D.vir

60926

9928

16%

9713

95.0

9816

95.6

9324

90.1

 

D.wil

60704

8628

14%

8528

95.5

8535

95.4

7420

80.5

 

D.yak

61272

51039

83%

50318

97.9

50244

97.8

50318

97.9

D.gri

D.moj

61933

22084

35%

20200

90.8

18586

83.4

22109

98.9

 

D.per

62029

8393

14%

8843

94.7

8068

88.6

8160

88.1

 

D.pse

61852

9328

15%

9325

94.0

8476

86.5

8675

87.6

 

D.sim

61844

8038

13%

8455

97.7

7624

89.8

7701

88.8

 

D.wil

62007

7638

13%

7380

88.1

6860

83.4

7586

93.4

 

D.yak

61729

8760

14%

8935

97.5

8112

89.7

8180

88.7

D.moj

D.per

67626

8068

13%

8403

94.4

7752

88.1

7844

88.8

 

D.pse

67781

9001

13%

8901

94.7

8141

87.3

8251

88.2

 

D.sim

67662

7831

12%

8153

96.5

7430

89.7

7528

89.6

 

D.wil

66834

7462

12%

7314

87.7

6870

84.4

7456

93.0

 

D.yak

67142

8580

13%

8721

95.8

7887

88.9

8068

88.7

D.per

D.sim

29281

8133

28%

8181

97.7

8093

97.1

8140

97.1

 

D.vir

29314

5133

18%

4897

91.9

4935

92.1

4871

91.3

 

D.wil

29300

4635

16%

4420

89.0

4382

88.8

4079

81.8

 

D.yak

29451

8534

29%

8478

97.6

8439

97.4

8403

96.6

D.pse

D.sim

59107

15465

27%

15776

97.7

15596

97.0

15592

96.6

 

D.vir

59041

9857

17%

9346

91.8

9393

92.1

9249

90.6

 

D.wil

59337

8938

15%

8582

90.2

8546

90.2

7757

81.8

 

D.yak

59277

16671

28%

16545

97.6

16474

97.3

16387

96.6

D.sim

D.vir

65022

8855

14%

8829

95.9

8867

93.6

8437

90.5

 

D.wil

64973

7943

12%

7921

95.3

7862

92.5

6864

80.1

 

D.yak

64934

46720

72%

45819

97.2

46188

96.5

45819

97.2

D.vir

D.yak

63073

8988

14%

8781

93.5

8851

93.6

8649

91.4

D.wil

D.yak

48969

6204

13%

5684

87.5

5748

87.8

5061

76.8

Median Mapping Ratio (%)

  

97.4

 

93.6

 

91.7

  1. Each row shows results for blocks of 200 nucleotides randomly chosen from the source genome. Results are shown for three different configurations for indirect translation that are depicted in Figure 2, namely, D.melanogaster-star, D.sechellia-star and the clade-center configuration, where in each case we report two items: (i) total number of blocks translated through the specified configuration (indirect) and (ii) the fraction of directly translated blocks that are matched by identical indirect translations. To compact the results, pairwise comparisons where at least one configuration would result in a direct comparison have not been included here. Also, the species are shown in abbreviated format; see Figure 2 for equivalent complete species name.