We also examined the power of our 10× sequencing to discover rare genotypes on the integrated array. The 10× sequencing in this sample discovered 7,567 of 10,328 singletons, or SNPs where the rare allele is observed only once (73%), 7,322 of 8,745 doubletons (84%), 8,367 of 8,809 tripletons (95%), and 3,886 of 3,966 quadrupletons (98%) on the integrated array. Of monomorphic sites on the integrated array, sequencing erred in a small fraction of instances, calling 2,515 of 150,329 monomorphic sites on this array as polymorphic (1.7%). While errors in variant discovery are likely due to sequencing errors, it is also possible that these errors are due to incorrect genotype calls on the integrated array, which can be more challenging for rare variants. In summary, 10× whole genome sequencing does reasonably well in genotyping singletons and other rare variants.
