PhyloTree Build 17 mutations, one per row

The mutations of every haplogroup in phylotree17, one row per mutation, in the order Haplogrep lists them, with the bases before and after worked out by following the tree from the RSRS.

Usage

phylotree17_mutations

Format

A data frame with 13,384 rows and 6 columns:

haplogroup

Haplogroup whose branch carries the mutation.

notation

The mutation as written by Haplogrep.

position

Position in the RSRS/rCRS coordinates.

type

transition, transversion, back-mutation, insertion or deletion.

ancestral

Base before the mutation (for a reverted insertion, the inserted sequence); NA for insertions.

derived

Base after the mutation, or the inserted sequence; NA for deletions and reverted insertions.

Source

See phylotree17.

Details

Seven back-mutations revert a position that nothing earlier on their path changes (six 16233C!, e.g. in D4c1b1, and D5a2 1438A!); for those the written base is taken as the result.

Examples

table(phylotree17_mutations$type)
#> 
#>    transition  transversion back-mutation     insertion      deletion 
#>         11268           533          1182           130           271 
phylotree17_mutations[phylotree17_mutations$haplogroup == "J1c", ]
#>      haplogroup notation position       type ancestral derived
#> 9463        J1c     185A      185 transition         G       A
#> 9464        J1c     228A      228 transition         G       A
#> 9465        J1c   14798C    14798 transition         T       C