Genotype concordance between 454-generated genotype calls and those directly genotyped via Illumina GoldenGate or Illumina 660 W.

Genotype calls are divided into two categories: all calls; or confident genotype calls based on Genotype Quality (GQ) ≥ 10. Call accuracy gives the concordance between the SNP genotype derived from 454 data and Illumina-generated data across all samples excluding missing data, and the call rate incorporates missing data on an individual basis. These are calculated for all genotypes, and heterozygous (het) calls only.