Originally Posted by
Zoro
I'm glad your getting the hang of it. Keep at it and you'll slowly get better ! Good to see that you were able to use the 1240K set.
I like your FST results better than F2s and I think you should use that more than F2s in the future for distances.
I see that Greek-2 and Bulgarians are closest to you but it looks like you split Greeks into individual samples whereas with Bulgarians it was the average of both Simons samples.
Can you split the Bulgarians and others into individual samples and repost for kicks
Fst, Bulgarian and Turkish also separated:
Code:
pop1 pop2 est se
1 Kaspias Adygei.DG 0.134 0.00285
2 Kaspias Albanian.DG 0.137 0.00395
3 Kaspias Bashkir.SG 0.136 0.00300
4 Kaspias Bulgarian_1.DG 0.126 0.00347
5 Kaspias Bulgarian_2.DG 0.130 0.00358
6 Kaspias Cretan.DG 0.131 0.00294
7 Kaspias French.DG 0.134 0.00274
8 Kaspias Greek_1.DG 0.130 0.00339
9 Kaspias Greek_2.DG 0.129 0.00364
10 Kaspias Iranian.DG 0.133 0.00292
11 Kaspias Italian_North.DG 0.132 0.00351
12 Kaspias Jordanian.DG 0.141 0.00279
13 Kaspias Mansi.DG 0.156 0.00283
14 Kaspias Polish.DG 0.135 0.00354
15 Kaspias Russian.DG 0.134 0.00293
16 Kaspias Tatar_Tomsk.SG 0.142 0.00294
17 Kaspias Turkish_1.DG 0.145 0.00381
18 Kaspias Turkish_2.DG 0.132 0.00348
19 Kaspias Turkmen.SG 0.135 0.00297
20 Kaspias Tuscan_1.DG 0.134 0.00296
21 Kaspias Uzbek.SG 0.140 0.00272
I do not get, how can I be closer to French and Adygei than Albanians? The rest seems ok though.
Your qpAdm model looks good ! but I'm interested to know how many SNPs in the extract and which pright you used
You're showing 25% Usbek -/+4% which is higher than what I got for the Iraqi Kurds and Kayseri Turks. The Iraqi Kurds were something like ~80% Armenian + ~20% Bashkir or Turkmen.
I like to model with moderns sometimes because it gives me an idea how shifted compared to their neighbors a population is
For ex Iraqi Kurds consistently get Iranian or Georgian or Armenian + 10% Estonian or some percentage Tatar or Bashkir. It doesn't mean that they have Estonian ancestry bu this tells me that a significant proportion of their ancestors came from NE of Armenia or Iran
How many SNPs did you end up with when you did your extract
Code:
√ 1578508 SNPs read in total
! 565741 SNPs remain after filtering. 540537 are polymorphic.
Let me show you all the models:
Right(Adygei, Cretan, Iranian, Mansi, Polish, Jordanian, Tatar_Tomsk, Italian_North, Albanian, French) -all the of Simeon's-
Code:
target left weight se z
1 Kaspias Bulgarian_1.DG 0.78 0.044 17.51
2 Kaspias Turkmen.SG 0.22 0.044 4.98
f4rank dof chisq p.value dofdiff chisqdiff p_nested
1 1 8 5.96 0.65119 10 553.51 1.6e-112
2 0 18 559.48 < 2e-16
Code:
target left weight se z
1 Kaspias Bulgarian_1.DG 0.76 0.048 15.89
2 Kaspias Bashkir.SG 0.24 0.048 4.89
f4rank dof chisq p.value dofdiff chisqdiff p_nested
1 1 8 6.44 0.59806 10 478.01 2.2e-96
2 0 18 484.45 < 2e-16
Code:
target left weight se z
1 Kaspias Bulgarian_1.DG 0.8 0.039 20.51
2 Kaspias Uzbek.SG 0.2 0.039 5.13
f4rank dof chisq p.value dofdiff chisqdiff p_nested
1 1 8 4.4 0.81917 10 796.21 1.3e-164
2 0 18 800.62 < 2e-16
Code:
target left weight se z
1 Kaspias Bulgarian_1.DG 0.82 0.044 18.83
2 Kaspias Tatar_Tomsk.SG 0.18 0.044 4.15
f4rank dof chisq p.value dofdiff chisqdiff p_nested
1 1 8 6.16 0.62951 10 628.79 1.2e-128
2 0 18 634.94 < 2e-16
I get negative scores when used Turkish samples to model my Turkic part, which might mean Turkic ancestors of Balkan Turks were not Anatolian Turkish-like.
Code:
target left weight se z
1 Kaspias Bulgarian_1.DG 1.04 5.3 0.2
2 Kaspias Turkish_1.DG -0.04 5.3 -0.01
f4rank dof chisq p.value dofdiff chisqdiff p_nested
1 1 8 28.18 0.00044187 10 36.1 0.000081
2 0 18 64.28 4.09e-07
Code:
target left weight se z
1 Kaspias Bulgarian_1.DG 11.44 364.26 0.031
2 Kaspias Turkish_2.DG -10.44 364.26 -0.029
f4rank dof chisq p.value dofdiff chisqdiff p_nested
1 1 8 29.87 0.00022259 10 30.66 0.00067
2 0 18 60.54 1.6747e-06
Reply With Quote
Bookmarks