Table 2. Mendelian inheritance of VNTRs in 1000 Genomes trios.
| Utah family | Nigerian family | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Daughter | Mother | Father | Loci | Incon- | Daughter | Mother | Father | Loci | Inconsistent | ||
| NA12878 | NA12892 | NA12891 | All | Diff | sistent | NA19240 | NA19238 | NA19239 | All | Diff | |
| 1241 | 1327 | 1402 | 274 | 20 | 1 | 1963 | 1979 | 1956 | 437 | 55 | 0 |
Shown are the number of VNTR loci for which two alleles were supported in each individual (sum of Same/Diff and Diff/Diff as in Table 3 C), number of loci in common for the trio (All), the subset of loci in common for which all three have different genotypes (Diff), and the number of loci inconsistent with Mendelian inheritance. The inconsistency count applies to all the loci in common, although the subset of loci for which all the family members are heterozygous AND have different genotypes provides the strongest test that VNTRseek is not systematically mis-assigning alleles from different loci to the same locus. Note that the VNTR loci with two alleles supported ranged from 46% to 52% of the total VNTRs in these individuals (data not shown). This contrasts with the lower coverage Watson genome in which 17% of loci exhibited two alleles.