Table 1: Summary of sample collections and sequencing metrics for the four main studies of the UK10K project

From: The UK10K project identifies rare variants in health and disease

Study name and designnSequencing strategy, mean read depth and Ts/Tv ratioSNVs/INDELsSNVs/INDELs by allele frequency
Cohorts. Unselected samples from two population-based cohorts3,781WGS, 7×
Ts/Tv = 2.15
42,001,210/3,490,825<1%: 34,247,969/2,296,962 1–5%: 2,298,220/412,168 >5%: 5,869,317/1,496,955
Rare. Eight rare diseases with expected different allelic architectures (ciliopathy, coloboma, congenital heart disease, familial hypercholesterolaemia, intellectual disability, neuromuscular, severe insulin resistance and thyroid disease)961 (397)WES, 77×
Ts/Tv = 3.02
252,809/ 1,621<1%: 171,564/1,384
≥1%: 81,245/237
Obesity. Severely obese children (BMI > 3 s.d. from population mean) and adults with extreme obesity1,468 (1,359)WES, 82×
Ts/Tv = 3.02
484,931/ 3,370<1%: 403,684/3,133
≥1%: 81,247/237
Neurodevelopmental. Autism and schizophrenia (individual probands, families with one affected and other healthy individuals sampled, families with data from multiple affected individuals and individuals with comorbid intellectual disability and psychosis)2,753 (1,707)WES, 77×
Ts/Tv = 3.02
538,526/ 3,826<1%: 457,278/3,589
≥1%: 81,248/237
  1. For the cohorts arm, numbers are for the set of 3,781 samples passing quality control, while a subset of 3,621 was used for association testing. For the exome arm, numbers of sites are based on the joint call set, and are calculated for a subset of all individuals that represent the patient subset (in brackets). The total number of individuals sequenced in each study is also given (see Supplementary Methods). The transition to transversion ratio (Ts/Tv) was calculated for the final set of SNVs excluding multiallelic sites. WGS, whole-genome sequencing; WES, whole-exome sequencing.