Table 1. Phasing statistics from fosmid pool sequencing.
| Population | Sample | Number of clones after filter | Number of blocks | N50 (kbp) | MEC value | Number of SNPs to be phased | Phased SNPs within blocks (%) | Number of blocks assigned parental allele | SNPs assigned parental allele (%) | Switch error count | Switch error corrected | Switch error rate (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| YRI | NA19240 | 521,783 | 16,334 | 347 | 37,143 | 2,588,454 | 92.94 | 15,171 | 92.74 | 586 | 421 | 0.091 |
| GWD | HG02799 | 1,141,020 | 5,236 | 1416 | 82,387 | 2,780,269 | 99.00 | 3,041 | 98.38 | 327 | 146 | 0.163 |
| ESN | HG03108 | 1,058,027 | 5,416 | 1294 | 77,499 | 2,756,725 | 99.07 | 3,323 | 98.45 | 258 | 115 | 0.127 |
| MKK | NA21302 | 892,863 | 6,097 | 1416 | 175,935 | 2,736,727 | 98.60 | 3,751 | 97.96 | 336 | 265 | 0.098 |
| MSL | HG03428a | 1,424,234 | 4,390 | 1849 | 167,294 | 2,775,099 | 99.30 | 3,549 | 97.90 | — | — | — |
| GIH | NA20847a | 571,419 | 16,838 | 385 | 44,870 | 1,680,704 | 93.37 | 13,319 | 90.98 | — | — | — |
| San | HGDP01029a | 358,759 | 17,695 | 228 | 27,712 | 2,623,001 | 87.10 | 16,516 | 89.15 | — | — | — |
| Mbuti | HGDP00456a | 381,075 | 18,465 | 242 | 28,629 | 2,517,569 | 78.70 | 17,385 | 81.72 | — | — | — |
We resolved haplotypes using fosmid pool sequencing. MEC is the number of entries to correct when resolving haplotypes. Switch errors are counted as the number of switches required to obtain the same haplotype phase when comparing inferred haplotype phase with true haplotype phase. Switch error rate is switch error normalized by number of variants for comparison.
a
Indicates samples that have had Prism applied to link adjacent blocks together.