Embedded Files
Monday, October 29, 2012
'globe13' calculator
'globe13' calculator
In national Geographic genomic: The pop
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.
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.
The globe13 calculator is based on the K=13 analysis.
It includes the following components:
k12b
Chromosome #SNPs
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
-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,
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
South_Asian 0.03
East_African 0.03
Southwest_Asian 2.62
East_Asian 8.73
Sub_Saharan 1.08
All 166770
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
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
'globe13' participant results
'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:
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.
I have also created a TreeMix plot using Palaeo_African as an outgroup, and allowing as many as 5 migration edges:
A neighbor-joining tree of the 13 components based on the Fst divergences:
Excellent explanation of breakdown of populations
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
Hardcore tools:
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
Page updated
Report abuse