Nature research paper: The sequences of 150,119 genomes in the UK Biobank
To identify functionally important regions, we started by estimating whether reliable basecalls can be expected to be made at each site in the genome. The sequence coverage at each base pair in GRCh38 was computed for each of the 1,000 randomly selected individuals. At each base pair, we then computed the mean and s.d. of coverage across the 1,000 individuals. Base pairs with mean coverage of at least 20 and s.d. coverage of at most 12 were considered reliable base pairs.
. We used this distribution on mutation classes to calculate the transition to tranversion ratio in each case.Saturation for general mutation classes We restricted our analysis to the reliable base pairs described above and grouped base pairs and their complement and considered each A or T base in the genome as a mutation opportunity for T>A, T>C or T>G mutations. Similarly, we considered each G or C base as a potential C>A, C>G or C>T mutation, splitting C>T into two classes based on whether they occur in a CpG context.
We assumed that methylation is strand symmetric and computed the methylation ratio for each CpG dinucleotide in a given tissue type by tabulating the number of reads supporting methylation or non-methylation in each dinucleotide, summing over all samples of a given tissue type and then computed the fraction of reads that support methylation.
We considered a site in a CpG dinucleotide on the reference genome methylated in the germ line if its methylation ratio was at least 0.7 in both testes and ovaries, and the combined depth was at least 20 for testes and 30 for ovaries, or 10 times the number of samples in each tissue type. This resulted in a list of 17,902,255 CpG dinucleotides, with 35,804,510 CpG>TpG mutation opportunities.
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