View Full Version : Question about R1a
My step father (who is deceased) was predicted to belong to R1a-Z2125 (a subclade of Eurasian Z93) by usually highly reliable yseq cladefinder tool. However I heard yseq has problem with this particular snp and gives lot of false reads for Z2125. Afaik, Gixajo was also predicted to be Z93>Z2125 and later (with a proper test) he turned out to be subclade of Z280, not Z93 at all.
As for Morely predictor, it just shows my step father to be broadly R1a-M417 and nothing specific.
There is ethnic Croat sharing the same surname as my step father who belongs to R1a>Z280>CTS1211>Y35>CTS3402, which is a usual Slavic subclade and most common type of R1a among Croats.
Their surname is specific for one region only and less common elsewhere, and my step father native region main haplogroup is R1a Z280, while Z93, especially such exotic "Pashtun-Tajik" branches such as Z2125 are unheard of.
In my opinion, my stepdad was likely under Z280 like other Coat sharing his surname and probably not Z93.
What do you think?
Your stepfather was the last of the Aryans... :odinsleipnir2:
Yeah, Z280 is of course much more likely in Croatia or anywhere in Europe for that matter.
vbnetkhio
12-08-2021, 04:37 PM
My step father (who is deceased) was predicted to belong to R1a-Z2125 (a subclade of Eurasian Z93) by usually highly reliable yseq cladefinder tool. However I heard yseq has problem with this particular snp and gives lot of false reads for Z2125. Afaik, Gixajo was also predicted to be Z93>Z2125 and later (with a proper test) he turned out to be subclade of Z280, not Z93 at all.
As for Morely predictor, it just shows my step father to be broadly R1a-M417 and nothing specific.
There is a ethnic Croat sharing the same surname as my step father who belongs to R1a>Z280>CTS1121>CTS3402, which is a usual Slavic subclade and most common type of R1a among Croats.
Their surname is specific for one region only and less common elsewhere, and my step father native region is pred. R1a Z280, while Z93, especially such exotic "Pashtun-Tajik" branches such as Z2125 are unheard of.
In my opinion, my stepdad is likely under Z280 like other Coat sharing his surname and probably not Z93.
What do you think?
afaik, Z93 in Europe is found in trace amounts except in some VUR groups, so statistically he's probably not Z93.
I read from Kyp other people too (on Anthrogenica maybe?) noticed yseq problem with false reads for Z2125. I wonder why is that.
gixajo
12-08-2021, 04:42 PM
My step father (who is deceased) was predicted to belong to R1a-Z2125 (a subclade of Eurasian Z93) by usually highly reliable yseq cladefinder tool. However I heard yseq has problem with this particular snp and gives lot of false reads for Z2125. Afaik, Gixajo was also predicted to be Z93>Z2125 and later (with a proper test) he turned out to be subclade of Z280, not Z93 at all.
As for Morely predictor, it just shows my step father to be broadly R1a-M417 and nothing specific.
There is a ethnic Croat sharing the same surname as my step father who belongs to R1a>Z280>CTS1211>CTS3402, which is a usual Slavic subclade and most common type of R1a among Croats.
Their surname is specific for one region only and less common elsewhere, and my step father native region is pred. R1a Z280, while Z93, especially such exotic "Pashtun-Tajik" branches such as Z2125 are unheard of.
In my opinion, my stepdad is likely under Z280 like other Coat sharing his surname and probably not Z93.
What do you think?
It seems that is quite usual that error. (Z2125 instread of other M417 subclades) using some commercial test autosomal raw data in cladefinder.
Someone warned me when they predicted me as Z2125, so it must be something common.
Then I tried a Yseq R1a super panel to know for sure my Ydna, I think you advised me to test with Yseq.
I really liked their way of working. Very close people and always ready to inform you of any detail.:thumb001:
reboun
12-08-2021, 04:46 PM
Apparently R1a-Z2125 is of Iranic origin. Predictor might have been wrong.
https://upload.wikimedia.org/wikipedia/commons/f/fc/Eurasia_R1a_Z2125.jpg
rothaer
12-08-2021, 05:11 PM
I read from Kyp other people too (on Anthrogenica maybe?) noticed yseq problem with false reads for Z2125. I wonder why is that.
I just asked Thomas Krahn, the owner of YSEQ, that is also into the cladefinder. I'm curious what he will say. Maybe there is some imputation and guesswork involved.
Arūnas
12-08-2021, 05:27 PM
thanks God it's a subclade of Eurasian Z93, on wikipedia I read that Roma people can have Z-93 in Croatia and Hungary
https://en.wikipedia.org/wiki/Haplogroup_R1a
rothaer
12-08-2021, 05:36 PM
It seems that is quite usual that error. (Z2125 instread of other M417 subclades) using some commercial test autosomal raw data in cladefinder.
Someone warned me when they predicted me as Z2125, so it must be something common.
Then I tried a Yseq R1a super panel to know for sure my Ydna, I think you advised me to test with Yseq.
I really liked their way of working. Very close people and always ready to inform you of any detail.:thumb001:
What raw data did you have?
Alenka
12-08-2021, 05:39 PM
My step father (who is deceased) was predicted to belong to R1a-Z2125 (a subclade of Eurasian Z93) by usually highly reliable yseq cladefinder tool. However I heard yseq has problem with this particular snp and gives lot of false reads for Z2125. Afaik, Gixajo was also predicted to be Z93>Z2125 and later (with a proper test) he turned out to be subclade of Z280, not Z93 at all.
As for Morely predictor, it just shows my step father to be broadly R1a-M417 and nothing specific.
There is ethnic Croat sharing the same surname as my step father who belongs to R1a>Z280>CTS1211>Y35>CTS3402, which is a usual Slavic subclade and most common type of R1a among Croats.
Their surname is specific for one region only and less common elsewhere, and my step father native region main haplogroup is R1a Z280, while Z93, especially such exotic "Pashtun-Tajik" branches such as Z2125 are unheard of.
In my opinion, my stepdad was likely under Z280 like other Coat sharing his surname and probably not Z93.
What do you think?
Same thing happened with the MyHeritage raw data of my father when I ran it on yseq cladefinder. He got a false Z2125.
When I made him take the 23andMe test he turned out to be CTS3402.
rothaer
12-08-2021, 05:44 PM
Thomas Krahn now told me this:
Cladefinder essentially looks for the longest consistent path with the YFull tree from the given derived and ancestral SNP results. Positive SNPs increase the scoring and negative SNPs that are inconsistent with the tree position decrease the scoring. The path with the highest score is considered as the most likely position on the tree. In a small link at the bottom we also give the second best position from the scoring.
The details can be found in the function getPathScores:
https://github.com/.../blob/master/Common/CommonMethods.py
There are a few unreliable SNPs in that area of R1a on the YFull tree that may throw off the scores due to bleeding over from highly similar X chromosome locations. Especially microarray data from low quality samples may have some significant noise which affects the scoring.
Btw. I find it surprising that negative tested SNPs that are inconsistent with the tree position do not exclude that position entirely.
Same thing happened with the MyHeritage raw data of my father when I ran it on yseq cladefinder. He got a false Z2125.
When I made him take the 23andMe test he turned out to be CTS3402.
Thanks a lot for this. Than I assume it's kind of safe bet my step father also belonged to CTS3402.
Thomas Krahn now told me this:
Cladefinder essentially looks for the longest consistent path with the YFull tree from the given derived and ancestral SNP results. Positive SNPs increase the scoring and negative SNPs that are inconsistent with the tree position decrease the scoring. The path with the highest score is considered as the most likely position on the tree. In a small link at the bottom we also give the second best position from the scoring.
The details can be found in the function getPathScores:
https://github.com/.../blob/master/Common/CommonMethods.py
There are a few unreliable SNPs in that area of R1a on the YFull tree that may throw off the scores due to bleeding over from highly similar X chromosome locations. Especially microarray data from low quality samples may have some significant noise which affects the scoring.
Btw. I find it surprising that negative tested SNPs that are inconsistent with the tree position do not exclude that position entirely.
I find it very surprising too, it should exclude!!
rothaer
12-08-2021, 06:40 PM
I heard of more such wrong Z93 > Z2125 predictions, that turned out to be Z280, but in the "worst" cases even M458.
I told this accumulation of specific cases to Thomas Krahn and he explained that the YSEQ predictor is completely (and seemingly automated) relying on YFull. He thinks actually the given SNP selection for Z280 (!) might be the problem. If there is some out of ancient DNA wrongly concluded SNPs among them and this is tested negative for a testee, then the score for the likelyhood of the Z280 branch is going far down and the Z93 branch with Z2125 can get the highest likelyhood score instead. He also told that there have been some wrong assumptions detected in the tree and it may also be hard to draw the applicable conclusions from ancient DNA, especially if you take the possibility of back and forth mutations into account. These things are not carved in stone, he said.
I heard of more such wrong Z93 > Z2125 predictions, that turned out to be Z280, but in the "worst" cases even M458.
I told this accumulation of specific cases to Thomas Krahn and he explained that the YSEQ predictor is completely (and seemingly automated) relying on YFull. He thinks actually the given SNP selection for Z280 (!) might be the problem. If there is some out of ancient DNA wrongly concluded SNPs among them and this is tested negative for a testee, then the score for the likelyhood of the Z280 branch is going far down and the Z93 branch with Z2125 gets the highest likelyhood score instead. He also told that there have been some wrong assumptions detected in the tree and it may also be hard to draw the applicable conclusions from ancient DNA, especially if you take the possibility of back and forth mutations into account. These things are not carved in stone, he said.
Is he planning to fix it? Is it even possible for him to do?
reboun
12-08-2021, 06:50 PM
Yes. He might be of Romani origin (Indo-Iranic connection). This is also another possibility other than predictor’s being wrong.
thanks God it's a subclade of Eurasian Z93, on wikipedia I read that Roma people can have Z-93 in Croatia and Hungary
https://en.wikipedia.org/wiki/Haplogroup_R1a
rothaer
12-08-2021, 06:56 PM
Is he planning to fix it? Is it even possible for him to do?
He actually said that this problem had to be adressed to YFull. From this I concluded that the YSEQ Cladefinder is automatically linked to the current YFull information. So no, he will not fix it as a separate "special solution" at the cladefinder and deviate from the YFull information.
Yes. He might be of Romani origin (Indo-Iranic connection). This is also another possibility other than predictor’s being wrong.
Piss off Durkish animal.
reboun
12-08-2021, 07:14 PM
Piss off Durkish animal.
Okay, but you should seek psychological help.
:)
reboun
12-08-2021, 07:36 PM
Olina got mad after I told her stepfather might have Romani ancestry. I advised her to seek psychological help, she unfriended me. Interesting, very interesting ;)
Olina got mad after I told her stepfather might have Romani ancestry. I advised her to seek psychological help, she unfriended me. Interesting, very interesting ;)
Leave my thread, donkey. Thanks.
Target: Stearsolina_step_father
Distance: 1.9517% / 1.95170006 | R2P
68.9 Polish_Podlaskie
31.1 Italian_Tuscan
Distance to: Stearsolina_step_father
3.01680294 Hungarian_North
3.12929705 Croat_North
3.68586489 Slovenian
4.00923933 Hungarian_Alföld
4.19652237 Slovak
4.22803737 Hungarian
4.55680809 Hungarian_Transdanubia+Budapest
4.80397752 Croat
5.00893202 Poland_Lemko
5.06759312 Croat_East
5.17273622 Ukrainian_Carpathian
5.99738276 Bosniak_Bosnia
6.12831951 Czech
6.14322391 Croat_West
6.43241790 Ukrainian_Galicia
7.33137777 Croat_South
7.78598099 Moldova_Ukrainian
7.87043836 Moldova_North
8.03473708 Bosniak
8.05677355 Csángó-Ceangău
8.56291422 Hungarian_Transylvania+Székely
8.63184221 Polish_Southeast
8.85250247 South_Polish
8.93376740 Sorb_Lusatia
9.00382141 Romania_Moldavia_North
reboun
12-08-2021, 08:01 PM
(GEDmatch results)
Main concern of my last post was not your stepfather’s GEDmatch results. It was posted to indicate the fact that you are of an “interesting” personality :D
Main concern of my last post was not your stepfather’s GEDmatch results. It was posted to indicate the fact that you are of an “interesting” personality :D
Fuck off from my threads, rootless mongrel.
reboun
12-08-2021, 09:00 PM
Fuck off from my threads, rootless mongrel.
Olina, I am sorry to say that but you are “pathetic”.
:P
Yes with Myheritage Data my Y-Dna was predicted as R-Z2125(yseq) but with 23andme it turned out i'm R-Z2122 which is a different branch of R1a-Z93. I dont know what causes this issue.
But I can confirm that this problem is real, especially the combo Z2125(yseq) and R1a-M417 (Morley)
Figaro
01-03-2022, 06:06 PM
This got me thinking about my own R1a as well- Morley also just predicts as R-M417, but does say the following SNP's are positive:
CLFY16971
CLFY18665
CLFY4959
CTS11948
CTS12028
CTS12091
CTS3229
CTS3622
CTS3944
CTS4557
CTS5808
CTS5815
CTS8626
F1857
FB1947
FB988
FGC10271
FGC12056
FGC199
FGC201
FGC24468
FGC38
FGC43
FGC54
FGC77
FN1317
FN495
FN833
L1346
L248
L486
L760
L88
L882
M1185
M1188
M1189
M1199
M1219
M1226
M1239
M1263
M1272
M141
M251
M2695
M288
M3639
M3691
M3698
M3707
M3735
M3749
M3771
M642
M672
M696
M705
M74
M9118
M9122
M9336
M96
M98
N12
P102
P103
P117
P222
P239
P32
P38
P80
PAGES00026
PAGES00029
PAGES00037
PAGES00038
PAGES00081
PF1580
PF2587
PF2669
PF2670
PF2673
PF2679
PF2686
PF2692
PF2703
PF2719
PF2720
PF2730
PF2771
PF2775
PF3558
PF3708
PF518
PF5505
PF5506
PF5861
PF5863
PF5870
PF5877
PF5896
PF5901
PF5915
PF5930
PF5934
PF5951
PF5963
PF5977
PF6036
PF6037
PF6050
PF6126
PF6147
PF6234
PF6240
PF6276
PF:14136291(A|G)
PF:14231292(A|G)
PF:14432928(A|G)
PF:14639427(C|A)
PF:14692227(C|T)
PF:14958218(C|T)
PF:14993358(G|A)
PF:15027529(T|G)
PF:15086183(C|G)
PF:16492547(T|C)
PF:16971648(G|T)
PF:18026855(A|G)
PF:18109555(A|C)
PF:18656508(C|G)
PF:18865298(T|C)
PF:18914441(T|C)
PF:19179540(A|G)
PF:21409706(C|G)
PF:21410840(T|G)
PF:22190371(G|A)
PF:22739367(C|T)
PF:23476936(T|G)
PF:28590278(A|G)
PF:28733101(G|C)
PF:2887824(A|C)
S118
S24307
S26596
S26597
S26598
S27130
S27150
S27154
S27177
S27244
S27310
S27390
S27470
S27500
S27554
S27700
U250
YSC0000222
YSC0000286
YSC0001265
Z11996
Z8133
Z8143
Z8146
Not sure if that means much?
Powered by vBulletin® Version 4.2.3 Copyright © 2025 vBulletin Solutions, Inc. All rights reserved.