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Table 1 Proportion of SNPs from each discovery method predicted to successfully validate on both an Illumina Infinium and an Affymetrix Axiom array using predictive modeling and simple filtering approaches

From: Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success

Discovery method

Predicted validation success (%)

Infinium

Axiom

Predictive

Filtering

Predictive

Filtering

BOWTIE2

75.7

45.6

83.3

61.7

BWA

72.1

39.7

78.5

54.6

NEWBLER

46.8

27.3

48.9

35.5

SWAP454

57.0

34.6

61.8

45.9