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Table 3 Summary of the in vitro SNP genotyping performance assessed in a panel of 96 individuals from five Eucalyptus species

From: High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

In vitro SNP performance assessed

Candidate genes

F0

F1

F2

F3

F4

Total counts

%

# SNPs tested by the GGGT

72

96

96

108

108

288

768

-

Average SNP Call Rate (%)

91.0

95.2

90.0

94.9

95.0

97.8

-

 

# SNP with Call rate ≥ 0.95

58

81

74

90

97

268

668

87.0

% SNP with Call rate ≥ 0.95

80.6

84.4

77.1

83.3

89.8

93.1

-

 

Average SNP GeneTrain score

0.61

0.68

0.66

0.71

0.67

0.72

-

 

# SNPs with GeneTrain score ≥ 0.40

64

90

90

100

101

278

723

94.1

% SNPs with GeneTrain score ≥ 0.40

88.9

93.8

93.8

92.6

93.5

96.5

-

 

Average SNP GC50 score

0.57

0.59

0.59

0.64

0.62

0.67

-

 

# SNPs with GC50 score ≥ 0.40

63

89

89

100

101

277

719

93.6

% SNPs with GC50 score ≥ 0.40

87.5

92.7

92.7

92.6

93.5

96.2

-

 

Average MAF of SNPs with MAF ≥ 0.05

0.26

0.24

0.25

0.26

0.25

0.27

-

 

# SNP with MAF > 0.05

51

48

55

75

74

205

508

66.1

% SNP with MAF > 0.05

70.8

50.0

57.3

69.4

68.5

71.2

-

 
  1. Averages and SNP counts above specific thresholds of SNP reliability parameters (Call Rate, GeneCall50, GeneTrain scores) and polymorphism (MAF) for SNPs in pre-selected candidate genes and for genome-wide SNPs selected with increasingly stringent in silico SNP selection and design requirements (F0 through F4 - see methods for details).