dna Geneology family


Welcome: 
For personal ethnic genetic composition - sleuthing involves looking at certain snp (single nucleotyde polymorphisms - basically certain lines of the dna - show mutations in these populations. these markers combine randomly between mother and father - so sleuthing can be done in generalities - but breaks down in specifics - perhaps it is because half the info is lost - each recombining - so smaller and smaller mutation sequences can be mapped.

In national Geographic genomic: The pop




Monday, October 29, 2012

'globe13' calculator

The globe13 calculator is based on the K=13 analysis.
 It includes the following components:

  • Siberian
  • Amerindian
  • West_African
  • Palaeo_African
  • Southwest_Asian
  • East_Asian
  • Mediterranean
  • Australasian
  • Arctic
  • West_Asian
  • North_European
  • South_Asian
  • East_African

Fst divergences between ancestral components can be found here.

You need to extract the contents of the RAR file to the 
working directory of DIYDodecad. You use it by following 
exactly the instructions of the DIYDodecad README, 
but always type 'globe13' instead of 'dv3' in these instructions. 
You can consult the spreadsheet for proportions of the 
13 components in different world populations.


'globe13' participant results

Project participant results for the globe13 calculator can be found in 
the spreadsheet. Population median results andFst divergences 
are also included.

Below, you can see the first two dimensions of an 
MDS plot of the 13 components:

neighbor-joining tree of the 13 components based on the Fst divergences:
I have also created a TreeMix plot using Palaeo_African as an outgroup, and allowing as many as 5 migration edges:
The actual tree is:


((West_African:0.00448794,(East_African:0.00506576,(((((East_Asian:0.0173284,Siberian:0.00732773):0.0027852,(Amerindian:0.026174,Arctic:0.0118342):0.00742092):0.0114738,Australasian:0.0488974):0.00266559,South_Asian:0.00734044):0.008089,(Southwest_Asian:0.00541405,((West_Asian:0.00620657,North_European:0.00657599):0.00311587,Mediterranean:0.00798949):0.00650328):0.0118925):0.0299627):0.00597674):0.00671186,Palaeo_African:0.0215931);
0.0640319 NA NA NA Palaeo_African:0.0215931 Australasian:0.0488974
0.270468 NA NA NA Australasian:0.0488974 East_Asian:0.0173284
0.185213 NA NA NA South_Asian:0.00734044 ((West_Asian:0.00620657,North_European:0.00657599):0.00311587,Mediterranean:0.00798949):0.00650328
0.129883 NA NA NA North_European:0.00657599 Amerindian:0.026174
0.138757 NA NA NA Arctic:0.0118342 (West_Asian:0.00620657,North_European:0.00657599):0.00311587


Terms of use: 'globe13', including all files in the downloaded RAR file is free for non-commercial personal use. Commercial uses are forbidden. Contact me for non-personal uses of the calculator.



-Globe 13: MAG 
---------------------------
 FINAL ADMIXTURE PROPORTIONS:
 ----------------------------
 
  0.23%  Siberian            
 17.35%  Amerindian          
  1.75%  West_African        
  0.00%  Palaeo_African      
  4.51%  Southwest_Asian     
  0.00%  East_Asian          
 37.06%  Mediterranean       
  0.00%  Australasian        
  0.58%  Arctic              
  9.24%  West_Asian          
 28.62%  North_European      
  0.62%  South_Asian         
  0.04%  East_African        
 
     CPU time =  330.27 sec

KEG and MAG Note identical proportions mediteranean and zero percent australasian,

MAG in addition to 17.35 Amerindian 
has total absence of paleoafrican
Interestingly KEG has trace elements of Amerindian: has total absence of West and East African

k12b
 Chromosome #SNPs 

Atlantic_Med                             34.03
North_European                     25.50 
Caucasus                                         10.86
Gedrosia                                      9.71
Siberian                                     4.93 
Northwest_African                  2.48  
Southeast_Asian                     0.00  

South_Asian                             0.03   
East_African                                     0.03 
Southwest_Asian                        2.62   
 East_Asian                                     8.73     

Sub_Saharan                             1.08
 All 166770          





















 FINAL ADMIXTURE PROPORTIONS: dv3
 ----------------------------
 
  5.94%  East_European       
 35.89%  West_European       
 29.82%  Mediterranean       
  0.11%  Neo_African         
  7.30%  West_Asian          
  2.45%  South_Asian         
  8.19%  Northeast_Asian     
  4.65%  Southeast_Asian     
  0.00%  East_African        
  2.27%  Southwest_Asian     
  2.09%  Northwest_African   
  1.29%  Palaeo_African      
 
     CPU time =  159.70 sec























Hardcore tools:

Excellent explanation of breakdown of populations

http://dodecad.blogspot.com/2012/01/k12b-and-k7b-calculators.html

Important to search for the word portrait that links to graphics of subpopulations like "french basque" that gives you exact mixes of the types in each population

Spreadsheet of K12b


     GLOBE 13: 25236 total iterations KEG
 1.000E-08 final dQ 
  ----------------------------
 FINAL ADMIXTURE PROPORTIONS:
 ----------------------------
 
  0.01%  Siberian            
  0.63%  Amerindian          
  0.00%  West_African        
  0.25%  Palaeo_African      
  3.99%  Southwest_Asian     
  0.22%  East_Asian          
 37.00%  Mediterranean       
  0.00%  Australasian        
  0.05%  Arctic              
  9.30%  West_Asian          
 46.39%  North_European      
  2.15%  South_Asian         
  0.00%  East_African        
 
     CPU time =  329.74 sec








 K12b     MAG   KEG Keg Vs Mag (relative)
 similar high   
 Atlantic Med     34 38.97+1/10th
 Gedrosia     9.71 8.18-1/10th
 Caucasus   10.86 11.78+1/10th
 Different High   
 North European 25.50 35.69 +1/3
Similar some   
 Southwest Asian 2.62 3.32    v similar
small component vs virtually absent   
 Siberian 4.93 0.82 (negligible) MAG only
 Northwest African 2.48 0.17 Mag Only
 Sub Saharan   
KG: k12b
132570 SNPs missing (no-call or absent)
  FINAL ADMIXTURE PROPORTIONS:
 ----------------------------
 
  8.18%  Gedrosia            
  0.82%  Siberian            
  0.17%  Northwest_African   
  0.00%  Southeast_Asian     
 38.97%  Atlantic_Med        
 35.69%  North_European      
  1.07%  South_Asian         
  0.00%  East_African        
  3.32%  Southwest_Asian     
  0.00%  East_Asian          
 11.78%  Caucasus            
  0.00%  Sub_Saharan         
 
     CPU time =  113.88 sec

 KG dv3.par test (k12b?
  9.28%  East_European       
 48.35%  West_European       
 26.94%  Mediterranean       
  0.00%  Neo_African         
 10.78%  West_Asian          
  1.31%  South_Asian         
  0.51%  Northeast_Asian     
  0.16%  Southeast_Asian     
  0.00%  East_African        
  2.31%  Southwest_Asian     
  0.36%  Northwest_African   
  0.00%  Palaeo_African      
-----------------------------------------------------------
 -- DIY Dodecad v 2.1 --------------------------------------
 ------------------------------------------------@@@@@@@----
 -- Copyright (c) 2011 Dienekes Pontikos -------@@-----@@---
 ------------------------------------------------------@@---
 -- More information: ---------------------------@@@@@@@----
 ----- Dienekes' Anthropology Blog -------------@@----------
 -------- http://dienekes.blogspot.com ---------@@----------
 ----- The Dodecad Ancestry Project ------------@@@@@@@@@---
 -------- http://dodecad.blogspot.com ----------------------
 -----------------------------------------------------------
 
        12 ancestral populations
    166462 total SNPs
      4281 flipped SNPs
     11628 heterozygous SNPs
         8 no-calls
    132883 absent SNPs
  0.201674 genotype rate
      mode genomewide
 
132891 SNPs missing (no-call or absent) ----------------------------
 FINAL ADMIXTURE PROPORTIONS:
 ----------------------------
 
 
     CPU time =  419.80 sec

 
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