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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