Table 4.
Genotype concordance between HapMap II genotypes and genotypes obtained based on the 1000 Genomes Pilot sequencing data using Thunder and HapSeq
| Number of homozygote reference sites | Number of heterozygote sites | Number of homozygote alternative sites | Total number of Sites | Absolute discordance change | Relative performance gain | |
|---|---|---|---|---|---|---|
| CEU | ||||||
| Site count | 940 896 | 568 106 | 380 727 | 1 889 729 | ||
| Thunder concord (%) | 98.39 | 97.04 | 97.28 | 97.76 | ||
| HapSeq concord (%) | 98.51 | 97.56 | 97.54 | 98.03 | 0.27 | 12 |
| YRI | ||||||
| Site count | 1 207 419 | 699 815 | 499 590 | 2 406 824 | ||
| Thunder concord (%) | 98.07 | 96.19 | 96.74 | 97.24 | ||
| HapSeq concord (%) | 98.19 | 96.73 | 96.93 | 97.50 | 0.26 | 9 |
Only 33 CEU and 35 YRI individuals both available to the 1000 Genomes Pilot Project and the HapMap project were used in the evaluation.