Table 2 Comparison of GA sequencing and Illumina 1M genotyping alleles

From: The diploid genome sequence of an Asian individual

  1. We classified both the array-based genotyped alleles and the alleles that were called by the Illumina Genome Analyser (GA) into four categories: (1) HOM ref. (homozygotes where both alleles are identical to the reference); (2) HOM mut. (homozygotes where both alleles differ from the reference); (3) HET ref. (heterozygotes where only one allele is identical to the reference); and (4) HET mut. (heterozygotes where both alleles differ from the reference and also differ from one another). The number of GA sequencing sites that are consistent with genotyping at both alleles, at one allele, or that are inconsistent at both alleles were categorized as 2, 1, and 0, respectively. The genotyping array primarily included the major alleles of the most common SNPs found in the human population, so very few alleles found in the BeadChip analysis were sorted into category 4.
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