Mikkel Meyer Andersen

Worldwide PowerPlex Y23 short tandem repeat data from 19,630 Y-chromosomes

Data from a worldwide collaborative effort (see URL), where 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI).

Reference

Purps J, Siegert S, et al. (2014). A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Science International: Genetics, Volume 12, 2014, p. 12-23. http://dx.doi.org/10.1016/j.fsigen.2014.04.008 and http://www.sciencedirect.com/science/article/pii/S1872497314000842

Current version: 2014-05-23

Usage instructions:

1. Download the R object file by clicking here
2. Move the file to the right directory (whatever that may be)
3. Open R and type:

   
           load('y23_2014-05-23.RData')
         

4. You now have a new object in R called y23

Object structure:

• population_statistics
  • Population: Name of population (y23$haplotypes$org$Population and y23$haplotypes$integer_alleles$db$Population maps to this).
  • Longitude: Representative longitude of the population.
  • Latitude: Representative latitude of the population.
  • Continent: Continent of the population.
  • Ethnos: Ethnic group of the population.
  • Subpopulation: Subpopulation of the population.
• rst
  • org
    • rst: Matrix of characters (the entries 0 a note that the estimated Rst values was negative and was set to 0).
    • sig: Matrix with + for significant Rst values (p < 0.0001) and a number for a non-significant p-value. This is Table S6 in the reference.
  • parsed
    • rst: Distance object from y23$rst$org$rst (0 a replaced by 0).
    • sig: Boolean (+ replaced by TRUE and numbers by FALSE).
• haplotypes
  • org: Original data corresponding to Table S1 in the reference.
  • integer_alleles
    • db: Database of integer alleles. Integer alleles are obtained by removing observations with one or more of the following: Null alleles (denoted by 0 in the original dataset, org), duplicate alleles and intermediate alleles. Note also that DYS385ab and DYS389II are removed (DYS389II.I = DYS389II - DYS389I is still available).
    • population: The populations corresponding to the observations in db, such that row i in db is from the population listed in entry i of population.