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Table 1 Core Collection evaluation scores for different K selected elements

From: Principal components analysis - K-means transposon element based foxtail millet core collection selection method

   

Group A

 

Group B

K

  

6

12

24

48

 

6

12

24

48

ANE

data 0

 

0.7924

0.7451

0.6851

0.6159

 

N/A

N/A

N/A

N/A

 

data I

 

0.7167

0.6478

0.574

0.4294

 

0.5283

0.4047

0.3218

0.2279

 

data II

 

0.5212

0.3944

0.3262

0.2007

 

0.7145

0.6496

0.5692

0.4367

 

data III

 

0.7338

0.6683

0.5725

0.4322

 

0.4978

0.4164

0.3126

0.2199

ENE

data 0

 

0.1911

0.2646

0.2574

0.2735

 

N/A

N/A

N/A

N/A

 

data I

 

0.2463

0.2886

0.2961

0.3584

 

0.4925

0.5548

0.6139

0.7087

 

data II

 

0.4204

0.5183

0.574

0.6379

 

0.2703

0.289

0.3065

0.3519

 

data III

 

0.1355

0.2516

0.3109

0.3145

 

0.4761

0.5329

0.6265

0.6776

E

data 0

 

0.9113

0.8894

0.9059

0.9069

 

N/A

N/A

N/A

N/A

 

data I

 

0.8851

0.888

0.8917

0.8879

 

0.7604

0.7767

0.7576

0.74

 

data II

 

0.7415

0.7671

0.7593

0.7587

 

0.8905

0.893

0.8815

0.8818

 

data III

 

0.9272

0.8957

0.894

0.8915

 

0.7603

0.7357

0.7395

0.7501

MD

data 0

 

16.5192

4.7198

2.6549

1.7699

 

N/A

N/A

N/A

N/A

 

data I

 

18.3746

9.894

2.1201

0.3534

 

0

0

0

0

 

data II

 

22.2615

13.7809

6.0071

1.4134

 

22.2615

13.0742

6.0071

1.4134

 

data III

 

24.7588

12.8617

1.9293

1.2862

 

7.1429

0

0

0

VD

data 0

 

27.4336

36.8732

41.0029

46.3127

 

N/A

N/A

N/A

N/A

 

data I

 

33.9223

45.2297

51.2367

53.3569

 

67.8571

67.8571

57.1429

50

 

data II

 

31.8021

38.8693

45.9364

56.1837

 

30.742

37.4558

44.1696

55.477

 

data III

 

35.6913

42.4437

53.6977

54.0193

 

50

53.5714

67.8571

67.8571

CR

data 0

 

29.7935

46.0177

57.8171

69.9115

 

N/A

N/A

N/A

N/A

 

data I

 

37.1025

55.1237

68.9046

81.9788

 

71.4286

85.7143

89.2857

100

 

data II

 

36.7491

47.7032

62.1908

77.7385

 

34.2756

45.9364

60.0707

77.0318

 

data III

 

41.4791

54.0193

73.6334

81.672

 

71.4286

85.7143

96.4286

96.4286

VR

data 0

 

27.6275

41.3319

54.425

66.2917

 

N/A

N/A

N/A

N/A

 

data I

 

32.6321

48.6972

63.4782

80.4787

 

76.7938

86.7248

91.9404

102.2757

 

data II

 

34.9972

46.2934

58.241

75.3076

 

30.9728

43.7712

55.211

74.2049

 

data III

 

38.7036

51.9165

70.2887

77.0397

 

78.3303

93.7485

96.6503

94.5884

CA

data 0

 

64.8968

73.0088

78.9086

84.9558

 

N/A

N/A

N/A

N/A

 

data I

 

68.5512

77.5618

84.4523

90.9894

 

85.7143

92.8571

94.6429

100

 

data II

 

68.3746

73.8516

81.0954

88.8693

 

67.1378

72.9682

80.0353

88.5159

 

data III

 

70.7395

77.0096

86.8167

90.836

 

85.7143

92.8571

98.2143

98.2143

  1. ANE, average distance between each original collection (MC) and nearest core collection (CC) sample; ENE, average distance between each CC sample and nearest CC sample; E, average distance between CC samples; MD, homogeneity test for means; VD, homogeneity test for variance; CR, coincidence rate; VR, variable rate; CA, coverage of allele. N/A, not possible to perform diferent-set comparison. With the exception of ANE and MD, higher values suggest better representation. Detailed description of the scoring system is provided in the text. Group A core collections where compared with their original collection dataset; contrarily, when possible, core collections in group B where compared to another equivalent original collection dataset
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BMC Genomic Data

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