Mitochondrial haplogroups represent sets of similar haplotypes defined by SNVs that arrose as a result of sequential accumulation of mutations during prehistoric human migrations. Here we plot haplogroup defining SNPs on the mitochondrial genome.
SNPs defining European mitochondiral haplogroups.
git clone https://github.com/sjfandrews/mtHg-SNPs-plot.git
Dependencies include: tidyverse, ggplot2, ggnewscale, pals
install.packages('tidyverse', 'ggplot2', 'ggnewscale', 'pals')
Haplgroup defining SNPs were obtained from Hi-MC (Smieszek, S. et al. 2018. Peerj) and FamilyTreeDNA, and are are avaliable in data/HiMC_mtSNPs.csv and scripts/FamilyTreeDNA_mtSNPs.R. These are not an exhaustive list of all haplogroup defining mtSNPs, but are focused on the major macro haplogroups used by Hi-MC.
Gene boundries for the Mitochondrial geneome were obtained from the Revised Cambridge Reference Sequence(rCRS) and are generated by scripts/mtDNAbdries.R.
Main plotting functions are avaliable in mtHgSNPs.R.
Code base was inspired by Stephen Turners Mitochondrial Solar Plot and by the GWAS Catalog ideogram.