Fig 1.
A. Simulation results of diversity measurements for derived and ancestral alleles (N: 100, mutation rate of 1 base pair per generation: 0.0001, recombination rate of 1 base pair per generation: 0.0001); B. Cumulative proportions of correct identification of ancestral alleles according to the generations and derived allele frequencies.
Table 1.
Numbers of analyzed variants and mean estimates of total haplotypes, including the derived and ancestral alleles, to identify the ancestral alleles in the human genome.
Fig 2.
Histograms of derived alleles based on various methods of ancestral allele identification (original data: allele frequency distribution from the sequencing data of the 1000 Genomes Project; sequence-alignment: derived allele frequency distribution by sequence-alignment; θ1: the derived allele frequency distribution by θ1 estimates; θ2: the derived allele frequency distribution by θ2 estimates; all: derived allele frequency distribution for the variants with all three methods concordant; any: derived allele frequency distribution for the variants with more than any two methods concordant).
Table 2.
Number of nucleotide substitutions for each type in the human genome (Rate: AT mutation rate bias; Expected GC: expected GC proportion from the AT mutation rate bias).
Table 3.
Summary of insertions and deletions in the human genome (ratio: deletion/insertion).
Fig 3.
Changes in deletion-to-insertion ratios (A) and GC proportions (B) depending on the size of inserted or deleted base pairs from 1~10 to >10.
Fig 4.
AT bias depending on derived allele frequencies: A. nucleotide substitutions; B. single base-pair insertions and deletions.
Fig 5.
Summary of derived alleles from QTL and GWAS variants: A. Types of nucleotide substitutions; B. Deletion-to-insertion ratios of QTL variants; C. GC proportions in insertions and deletions of QTL variants (original: whole genome data; EUR exon: EUR exon-expression QTL data; YRI exon: YRI exon-expression QTL data; EUR gene: EUR gene-expression QTL data; EUR repeats: EUR transcribed repeats QTL data; EUR trratio: EUR transcription ratio QTL data; GWAS: GWAS catalog data).