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View Full Version : 307 Y chromosomes (by Estonian Biocentre) includes rare Croatian Q-Y6793



lgmayka
03-10-2015, 10:35 PM
The Estonian Biocentre recently released 307 high-coverage Y chromosome sequences. According to the provided metainfo spreadsheet (http://evolbio.ut.ee/chrY/Y_data_metainfo.xlsx), one of them was a Q1d from Mostar, Croatia. (The authors have apparently constructed their own incompatible haplotree, which is not available to us yet.) The data for this Q1d is in folder GS000020363-DID.

I extracted the vcfBeta file, and found that this sample was derived at
Y6793
Y6847
M2520

Thus, he clearly belongs to the rare Q-Y6793 (http://yfull.com/tree/Q-Y6793/), for which YFull has a Bosnian Big Y example (as well as a research sample labeled Sri Lankan Tamil in the UK).

soulblighter
03-10-2015, 10:49 PM
The Estonian Biocentre recently released 307 high-coverage Y chromosome sequences. According to the provided metainfo spreadsheet (http://evolbio.ut.ee/chrY/Y_data_metainfo.xlsx), one of them was a Q1d from Mostar, Croatia. (The authors have apparently constructed their own incompatible haplotree, which is not available to us yet.) The data for this Q1d is in folder GS000020363-DID.

I extracted the vcfBeta file, and found that this sample was derived at
Y6793
Y6847
M2520

Thus, he clearly belongs to the rare Q-Y6793 (http://yfull.com/tree/Q-Y6793/), for which YFull has a Bosnian Big Y example (as well as a research sample labeled Sri Lankan Tamil in the UK).


Australian Aboriginal I1a and E2a!!
The Iranian G2a4 is very interesting to me pereonally for obvious reasons.

newtoboard
03-11-2015, 12:19 AM
Didn't realize there was a Q1d. (only thought it was mostly Q1a and Q1b). I remember looking at this study and it also showed something called I3. Was that an error or a real new y dna?

lgmayka
03-11-2015, 01:50 AM
I extracted the vcfBeta file, and found that this sample was derived at
Y6793
Y6847
M2520

I now notice that the Estonian sequences also include a so-called Q1d from Nepal. Sure enough, he has the three SNPs listed above, and so is also Q-Y6793.

YFull's Bosnian example (YF02110) has 63 reliable novel SNPs (44 best, 19 acceptable). The Croatian Q1d (among the Estonian sequences) shares 55 of those 63.

lgmayka
03-11-2015, 01:51 AM
Didn't realize there was a Q1d. (only thought it was mostly Q1a and Q1b). I remember looking at this study and it also showed something called I3. Was that an error or a real new y dna?
The authors have made up their own haplotree. Their Q1d is our Q-Y6793. But I suspect the I3 really is something new.

Шад
03-11-2015, 08:35 PM
Paleo-Eskimo Saqqaq was Q-YP1500 (my small study).
Q-YP1500 is new subbranch, which unite eskimos of Alaska, Canada, Grenland and native population of Russian Far East.
http://goo.gl/vPhevo

Шад
03-11-2015, 08:42 PM
The Estonian Biocentre recently released 307 high-coverage Y chromosome sequences. According to the provided metainfo spreadsheet (http://evolbio.ut.ee/chrY/Y_data_metainfo.xlsx), one of them was a Q1d from Mostar, Croatia. (The authors have apparently constructed their own incompatible haplotree, which is not available to us yet.) The data for this Q1d is in folder GS000020363-DID.

I extracted the vcfBeta file, and found that this sample was derived at
Y6793
Y6847
M2520

Thus, he clearly belongs to the rare Q-Y6793 (http://yfull.com/tree/Q-Y6793/), for which YFull has a Bosnian Big Y example (as well as a research sample labeled Sri Lankan Tamil in the UK).

A new branch of Q-YP1600 under Q-Y6793.
Below SNPs common to YF02110 (BIH) and croat11 (Croatia):
YP1571-YP1625.

lgmayka
03-12-2015, 02:45 PM
According to the provided metainfo spreadsheet (http://evolbio.ut.ee/chrY/Y_data_metainfo.xlsx), one of them was a Q1d from Mostar, Croatia.
Although the sample is indeed ethnically Croatian, the city of Mostar is in Bosnia-Herzegovina.

ADW_1981
03-12-2015, 03:46 PM
The authors have made up their own haplotree. Their Q1d is our Q-Y6793. But I suspect the I3 really is something new.

My hunch is that it's I2c, the type of low-moderate frequency in Europe and Caucasus. I believe one of the Motalas was retested in Haak and it was part of this clade. I really need to double check that though.

lgmayka
03-12-2015, 04:49 PM
My hunch is that it's I2c, the type of low-moderate frequency in Europe and Caucasus.
Bernie Cullen wrote to the Haplogroup I mailing list:
---
We briefly checked the "I3" sample (35473) from Abkhazia, Georgia in the Estonian Biocentre data.

As Ken [Nordtvedt] predicted, it is M438+,

L596+ (14197631 C to T),

L597+,

PF3827+ (22444387 T to A)

so it is I2c2 according to the ISOGG tree
---

ADW_1981
03-12-2015, 05:55 PM
Is there a way to look at these SNPs without downloading a 7 gig file to my HDD? I might be looking at the wrong files on the server.

lgmayka
03-12-2015, 06:06 PM
Is there a way to look at these SNPs without downloading a 7 gig file to my HDD? I might be looking at the wrong files on the server.
Look for the vcfBeta file. It is fairly small, and readable by Excel.

Шад
03-14-2015, 05:45 PM
307 Y chromosomes (by Estonian Biocentre)
Argentina (Andean-Cachi):
Cachi3 - Q-Z5910 (M848+, Z5908+, Z5910+)
Cachi4 - Q-M848* (M848+)
Cachi5 - Q-Z5907* (M848+, Z5906+, Z5907+)

http://yfull.com/tree/Q-M848/
https://en.wikipedia.org/wiki/Cachi_Department

brygian
04-11-2015, 06:39 PM
Personal Genome Project has started releasing data again. PGP212 is Q1b1a1a1a1 - FGC1929/Y2200+, FGC1890/Y2231+, FGC1903/Y2221+, FGC1914/Y2212+, FGC1923/Y2203+, FGC1932/Y2198+, FGC1933/Y2197+, FGC7663+. I didn't check if he is negative for the other SNPs on that level or if they are no-calls. It may turn out that this sample splits Q1b1a1a1a1 in two. Somebody with more knowledge of this haplogroup should have a look.

Táltos
04-12-2015, 03:08 AM
Personal Genome Project has started releasing data again. PGP212 is Q1b1a1a1a1 - FGC1929/Y2200+, FGC1890/Y2231+, FGC1903/Y2221+, FGC1914/Y2212+, FGC1923/Y2203+, FGC1932/Y2198+, FGC1933/Y2197+, FGC7663+. I didn't check if he is negative for the other SNPs on that level or if they are no-calls. It may turn out that this sample splits Q1b1a1a1a1 in two. Somebody with more knowledge of this haplogroup should have a look.

Hopefully Шад our Q1b expert will see your post, and let us know. Or maybe lgmayka can decipher it for us?

Шад
04-12-2015, 07:33 PM
Hopefully Шад our Q1b expert will see your post, and let us know. Or maybe lgmayka can decipher it for us?

I will do this and let you know the result.

Шад
04-13-2015, 05:05 AM
Personal Genome Project has started releasing data again. PGP212 is Q1b1a1a1a1 - FGC1929/Y2200+, FGC1890/Y2231+, FGC1903/Y2221+, FGC1914/Y2212+, FGC1923/Y2203+, FGC1932/Y2198+, FGC1933/Y2197+, FGC7663+. I didn't check if he is negative for the other SNPs on that level or if they are no-calls. It may turn out that this sample splits Q1b1a1a1a1 in two. Somebody with more knowledge of this haplogroup should have a look.

PGP212 is Q-YP1004
About Q-YP1004 - page 92 at Gurianov at al. 2015
https://www.academia.edu/11738905/Clarification_of_Y-DNA_Haplogroup_Q1b_Phylogenetic_Structure_Based_on _Y-Chromosome_Full_Sequencing

Táltos
04-13-2015, 01:13 PM
PGP212 is Q-YP1004
About Q-YP1004 - page 92 at Gurianov at al. 2015
https://www.academia.edu/11738905/Clarification_of_Y-DNA_Haplogroup_Q1b_Phylogenetic_Structure_Based_on _Y-Chromosome_Full_Sequencing

Шад thank you very much for taking the time to let us know. I was not sure if this was a sample that you knew about or not. Good to see some Q-YP1004. I hope the other guys in the Haplogroup Q project that did not test BIG Y or FGC are checking to see if they are positive for some of these new SNPs.