Table 3

Discordant calls

Discordant calls


All disagreements

1,766 (6.86%)

GT-het>Seq-hom

1,720 (6.68%)

Seq-het>GT-hom

10 (0.03%)

Different homozygotes

15 (0.06%)

Different heterozygotes

5 (0.02%)

Seq-SNP>GT-Ref

16 (0.09%)


Comparison of the SNP calls made from genotype data and the sequence: discordant calls. GT-het>Seq-hom indicates a heterozygote under-call by MAQ (array based genotype heterozygote, MAQ based genotype homozygote). Seq-het>GT-hom indicates a possible heterozygote under-call by the array (array-based genotype homozygote for the reference allele, MAQ based genotype heterozygote). Different homozygotes denote homozygous genotypes on both platforms that both differed from the reference genotype. Different heterozygotes denote heterozygote genotypes on both platforms where one allele differs. Seq-SNP>GT-Ref indicates a MAQ based genotype that differs from the reference sequence while the chip based genotype displayed only the reference allele.

Eck et al. Genome Biology 2009 10:R82   doi:10.1186/gb-2009-10-8-r82

Open Data