MOESM1 of Population size influences the type of nucleotide variations in humans

2019-12-06T04:43:17Z (GMT) by Sankar Subramanian
Additional file 1: Figure S1. Correlation between effective population size (Ne) and the ratio AT→GC to GC→AT (b) estimated for homozygous SNVs from whole genomes of the 1000 Genomes Project. The relationship was highly significant (P < 10-6). Figure S2. Relationship between the effective population size (Ne) and the ratio of nucleotide changes within the same types (b): (A) within strong types i.e. C®G/G®C (B) within weak types i.e. A®T/T®A. The ratios were estimated using the high frequency SNVs (DAF > 0.9) belonging to 27 populations obtained from the 1000 genome Project. Figure S3. Relationship between the effective population size (Ne) and the ratio of nucleotide changes within the same types (b): (A) within strong types i.e. C→G/G→C (B) within weak types i.e. A→T/T→A. The ratios were estimated using the homozygous SNVs belonging to 126 populations obtained from the Simon Genome Project. Figure S4. Relationship between the effective population size (Ne) and the normalized ratio of AT®GC to GC®AT (b’) changes using equation 2 (see methods). We used A↔T and G↔C to normalize AT→GC and GC→AT changes respectively. (A) High frequency SNVs (DAF>0.9) and (B) Homozygous SNVs of the 1000 genome project (C) Homozygous SNVs from the Simons Genome Diversity project. The relationships were highly significant (P < 10-6). Figure S5. The relationship between effective population size (Ne) and the normalized ratio AT→GC/GC→AT (b) estimated for homozygous SNVs present in individual genomes belonging to 126 distinct populations of the world. This is very similar to Fig 4A except that the nucleotide diversities of non-Africans were 5% reduced while calculating Ne in order to neutralize the difference in mutation accumulation rates between Africans and non-Africans as reported recently. The correlation was highly significant (P < 10-6).