Table 2.
Median estimated efficacy and coverage of the human genome (excluding the Y chromosome) in different populations, provided by different marker sets.
| Population | Marker set | Full genomic sequence | ‘Coding’ regions | ||||
|---|---|---|---|---|---|---|---|
| τ (interquartile range) | C0.5 | C0.8 | τ (interquartile range) | C0.5 | C0.8 | ||
| CEU | HapMap (total) | 0.71 (0.57–0.84) | 83% | 33% | 0.7 (0.55–0.83) | 82% | 30% |
| Affymetrix 100K | 0.26 (0.11–0.47) | 23% | 7% | 0.23 (0.09–0.44) | 20% | 5% | |
| Affymetrix 500K | 0.52 (0.35–0.69) | 53% | 13% | 0.5 (0.34–0.67) | 50% | 12% | |
| Illumina 100K | 0.37 (0.21–0.58) | 33% | 9% | 0.44 (0.27–0.63) | 42% | 10% | |
| Illumina 300K | 0.55 (0.4–0.71) | 59% | 14% | 0.54 (0.39–0.7) | 58% | 13% | |
| Illumina 550K | 0.6 (0.45–0.75) | 68% | 18% | 0.6 (0.44–0.74) | 66% | 17% | |
| YRI | HapMap (total) | 0.74 (0.62–0.85) | 91% | 36% | 0.73 (0.61–0.84) | 90% | 34% |
| Affymetrix 100K | 0.25 (0.1–0.45) | 21% | 6% | 0.22 (0.08–0.42) | 19% | 5% | |
| Affymetrix 500K | 0.53 (0.38–0.69) | 55% | 13% | 0.51 (0.37–0.68) | 53% | 12% | |
| Illumina 100K | 0.29 (0.15–0.49) | 24% | 7% | 0.37 (0.22–0.56) | 32% | 7% | |
| Illumina 300K | 0.52 (0.37–0.68) | 53% | 12% | 0.51 (0.36–0.67) | 52% | 11% | |
| Illumina 550K | 0.59 (0.45–0.74) | 67% | 16% | 0.58 (0.44–0.73) | 65% | 15% | |
| JPT + CHB | HapMap (total) | 0.68 (0.52–0.82) | 77% | 28% | 0.67 (0.51–0.81) | 76% | 26% |
| Affymetrix 100K | 0.22 (0.08–0.42) | 19% | 6% | 0.19 (0.06–0.39) | 17% | 5% | |
| Affymetrix 500K | 0.48 (0.31–0.66) | 47% | 12% | 0.47 (0.3–0.65) | 45% | 11% | |
| Illumina 100K | 0.27 (0.12–0.47) | 23% | 7% | 0.34 (0.18–0.54) | 29% | 7% | |
| Illumina 300K | 0.5 (0.33–0.67) | 50% | 12% | 0.49 (0.33–0.66) | 48% | 11% | |
| Illumina 550K | 0.56 (0.39–0.72) | 60% | 15% | 0.55 (0.38–0.71) | 58% | 14% | |
| CEU | Hyp. Affymetrix 100K | 0.50 (0.32–0.68) | 50% | 12% | 0.47 (0.29–0.65) | 46% | 10% |
| Hyp. Affymetrix 500K | 0.64 (0.49–0.78) | 73% | 22% | 0.62 (0.47–0.76) | 71% | 19% | |
| Hyp. Illumina 100K | 0.46 (0.25–0.63) | 44% | 7% | 0.44 (0.24–0.62) | 42% | 7% | |
| Hyp. Illumina 300K | 0.62 (0.46–0.76) | 70% | 19% | 0.60 (0.44–0.74) | 67% | 17% | |
| Hyp. Illumina 550K | 0.66 (0.52–0.79) | 77% | 24% | 0.65 (0.50–0.78) | 75% | 21% | |
| YRI | Hyp. Affymetrix 100K | 0.55 (0.36–0.71) | 57% | 14% | 0.52 (0.33–0.69) | 53% | 12% |
| Hyp. Affymetrix 500K | 0.69 (0.57–0.8) | 85% | 26% | 0.68 (0.55–0.79) | 82% | 23% | |
| Hyp. Illumina 100K | 0.51 (0.32–0.69) | 52% | 13% | 0.49 (0.3–0.67) | 48% | 11% | |
| Hyp. Illumina 300K | 0.66 (0.53–0.78) | 79% | 22% | 0.64 (0.5–0.77) | 75% | 19% | |
| Hyp. Illumina 550K | 0.69 (0.57–0.8) | 85% | 26% | 0.68 (0.55–0.79) | 83% | 23% | |
| JPT+CHB | Hyp. Affymetrix 100K | 0.42 (0.2–0.63) | 40% | 10% | 0.4 (0.19–0.6) | 37% | 9% |
| Hyp. Affymetrix 500K | 0.6 (0.42–0.76) | 65% | 19% | 0.59 (0.4–0.74) | 63% | 17% | |
| Hyp. Illumina 100K | 0.4 (0.18–0.61) | 37% | 10% | 0.38 (0.16–0.58) | 35% | 8% | |
| Hyp. Illumina 300K | 0.53 (0.28–0.71) | 54% | 15% | 0.51 (0.27–0.69) | 52% | 13% | |
| Hyp. Illumina 550K | 0.59 (0.4–0.74) | 63% | 15% | 0.58 (0.39–0.73) | 62% | 14% | |
All estimates refer to NCBI build 35, excluding annotated gaps, centromers, heterochromatin and telomers. ‘Coding’ regions were defined by the ‘RefSeqs’ provided in the Golden Path (http://genome.ucsc.edu), including introns, exons and 10 kb of flanking sequence.
τ genome-wide median of the relative efficacy; C0.5, (C0.8): percentage of the autosomal genome covered with τ ≥ 0.5 (τ ≥ 0.8); Hyp.: hypothetical.