Extended Data Table 3. Counts and properties of variants identified in sequenced subjects.
a. Variant numbers for the 2,657 individuals with whole genome sequence data passing QC and included in the association analysis data set; b. Variant numbers are provided for the 13,008 individuals passing initial rounds of QC from which further QC defined the 12,940 subjects included in the association analysis data set. Private refers to variants seen in only a single ancestral group; cosmopolitan to variants seen in all five major ancestral groups.
| a | |||
|---|---|---|---|
| Genomes integrated panel | |||
| SNV | Indel | SV | |
|
Variant
Type N (%total) |
25.2M (94%) | 1.50M (5.6%) | 8,876 (0.03%) |
| Coding | Non-coding | ||
|
Function N (%total) |
888K (3.3%) | 25.8M (97%) | |
| Rare (MAF<0.5%) | Low frequency (0.5<MAF<5%) | Common (MAF>5%) | |
|
Frequency
spectrum N (%total) |
6.26M (23%) | 4.16M (16%) | 16.3M (61%) |
| b137 | Novel | ||
|
dbSNV N (%total) |
14.6M (55%) | 12.1M (45%) | |
| b | ||||||
|---|---|---|---|---|---|---|
| Exome sequence data | ||||||
| All samples | African-American | East-Asian | European | Hispanic | South-Asian | |
| Samples: | 13,008 | 2,086 | 2,165 | 4,579 | 1,959 | 2,219 |
| T2D cases | 6,504 | 1,018 | 1,012 | 2,359 | 1,021 | 1,094 |
| T2D controls | 6,436 | 1,056 | 1,153 | 2,182 | 922 | 1,123 |
| Excluded from association analysis | 68 | 12 | 0 | 38 | 16 | 2 |
| Coverage: | ||||||
| Coding: | ||||||
| Mean (Mc) per gene | 81.7 ±23.7 | 83.2 ±24.0 | 84.6 ±23.8 | 78.6 ±23.3 | 83.8 ±24.1 | 78.2 ±23.2 |
| # of genes with Mc <20 | 368 | 302 | 302 | 351 | 269 | 325 |
| Non-coding: | ||||||
| Mean per gene | 59.0 ±21.0 | 60.9 ±21.5 | 62.2 ±21.6 | 57.5 ±20.6 | 59.2 ±21.2 | 55.4 ±20.3 |
| # of genes with Mc <20 | 1,150 | 738 | 731 | 1,102 | 804 | 945 |
| Variant annotations: | ||||||
| Synonymous SNV | 627,630 | 237,430 | 178,232 | 192,282 | 156,231 | 211,218 |
| Missense SNV | 1,110,897 | 354,797 | 296,707 | 327,049 | 231,351 | 344,191 |
| Start SNV | 2,055 | 593 | 523 | 639 | 384 | 583 |
| Nonsense SNV | 26,321 | 7,188 | 6,668 | 8,030 | 4,660 | 7,339 |
| Frameshift INDEL | 26,901 | 6,605 | 6,159 | 7,515 | 4,155 | 6,609 |
| Inframe INDEL | 11,090 | 3,471 | 2,963 | 3,145 | 2,068 | 3,165 |
| 3′UTR SNV, INDEL | 65,013 | 24,583 | 19,149 | 21,102 | 16,959 | 22,177 |
| 5′UTR SNV, INDEL | 43,965 | 16,920 | 13,520 | 15,562 | 11,634 | 15,595 |
| Intron SNV, INDEL | 931,449 | 352,398 | 270,564 | 296,970 | 243,139 | 314,810 |
| Essential splicing SNV, INDEL | 14,286 | 3,648 | 3,454 | 4,108 | 2,301 | 3,744 |
| Other splicing SNV, INDEL | 128,644 | 45,876 | 35,413 | 38,263 | 30,301 | 41,122 |
| Non-coding RNA SNV, INDEL | 18,113 | 7,247 | 5,996 | 6,715 | 5,084 | 6,706 |
| Intergenic SNV, INDEL | 37,345 | 14,335 | 11,498 | 13,614 | 10,700 | 12,937 |
| All | 3,043,709 | 1,075,091 | 850,846 | 934,994 | 718,967 | 990,196 |
| Coding frequency spectrum: | ||||||
| Rare (MAF<0.5%) | 95.79% | 83.30% | 90.06% | 89.19% | 84.56% | 89.89% |
| private | 77.93% | 53.79% | 65.47% | 51.80% | 37.26% | 61.55% |
| cosmopolitan | 0.35% | 1.80% | 3.02% | 1.88% | 2.24% | 1.73% |
| Low frequency (0.5<MAF<5%) | 2.57% | 10.36% | 4.61% | 5.52% | 8.21% | 5.10% |
| private | 0.17% | 1.43% | 1.10% | 0.26% | 0.52% | 1.02% |
| cosmopolitan | 0.60% | 1.50% | 1.54% | 1.94% | 2.74% | 1.62% |
| Common (MAF>5%) | 1.65% | 6.35% | 5.33% | 5.29% | 7.23% | 5.00% |
| private | 0.09% | 0.00% | 0.00% | 0.00% | 0.01% | 0.00% |
| cosmopolitan | 1.50% | 4.35% | 5.17% | 4.97% | 6.88% | 4.86% |
| Intron/UTR frequency spectrum: | ||||||
| Rare (MAF<0.5%) | 94.09% | 78.68% | 86.91% | 86.17% | 81.43% | 86.68% |
| private | 74.76% | 49.81% | 61.36% | 45.26% | 31.03% | 56.96% |
| cosmopolitan | 0.46% | 2.07% | 3.98% | 2.49% | 2.66% | 2.19% |
| Low frequency (0.5<MAF<5%) | 3.52% | 12.57% | 5.63% | 6.51% | 9.43% | 6.32% |
| private | 0.25% | 1.74% | 1.25% | 0.29% | 0.47% | 1.18% |
| cosmopolitan | 0.80% | 1.81% | 2.11% | 2.53% | 3.30% | 2.17% |
| Common (MAF>5%) | 2.39% | 8.76% | 7.46% | 7.32% | 9.14% | 7.00% |
| private | 0.15% | 0.00% | 0.00% | 0.01% | 0.00% | 0.00% |
| cosmopolitan | 2.17% | 5.94% | 7.26% | 6.93% | 8.77% | 6.81% |