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homosapien
06-02-2017, 06:54 PM
Hi

Can someone please help me with what is the BY2835 SNP, which I seem to be positive for, however there is no haplogroup for it.

Thanks,

homosapien
06-21-2017, 05:52 PM
Wanted to update this thread for future reference in case someone else turns up BY2835.

I have no haplogroup associated with BY2835, even though I am positive for it.

As a matter of fact as the test progressed further I happen to be R1a-Z93-L657-Y6-Y920. Which was formed 4700 years ago. Negative for Y928.

https://www.yfull.com/tree/R-Y920/

The test is still in the works , checking for Y906 and YP5633.

parasar
06-21-2017, 07:55 PM
Hi

Can someone please help me with what is the BY2835 SNP, which I seem to be positive for, however there is no haplogroup for it.

Thanks,

Do you know why this SNP was tested?
Was this part of the Z93 panel?

Rethel
06-21-2017, 08:30 PM
Is there some cumulate data about Z93 by country?

Amerijoe
06-21-2017, 09:40 PM
Hi

Can someone please help me with what is the BY2835 SNP, which I seem to be positive for, however there is no haplogroup for it.

Thanks,

Homosapien, ran BY2835 through my yfull snp search and this is what it indicates.

17124

Amerijoe
06-21-2017, 10:00 PM
Is there some cumulate data about Z93 by country?

Here is a percentage distriution list from livingdna. I had asked for the studies related to their findings and received a response indicating readily available info. I guess they consider this to be priory info and are not ready to decimate their methods. Some results seem questionable. Someone with better understanding and knowledge may want to elaborate.

1712517126

homosapien
06-21-2017, 10:03 PM
Do you know why this SNP was tested?
Was this part of the Z93 panel?

Yep, it was part of the Z93 panel. Though how is not clear. It was the first SNP to appear positive, which was followed by the Y6 and downwards in batches.

homosapien
06-21-2017, 10:14 PM
Here is a percentage distriution list from livingdna. I had asked for the studies related to their findings and received a response indicating readily available info. I guess they consider this to be priory info and are not ready to decimate their methods. Some results seem questionable. Someone with better understanding and knowledge may want to elaborate.

1712517126

I think those numbers might be understated excessively due to under sampling. Most studies put the R1a frequency around 15 to 17% of India's male lineages. Which would be approximately 100 mil.

Rethel
06-21-2017, 10:23 PM
Here is a percentage distriution list from livingdna. I had asked for the studies related to their findings and received a response indicating readily available info. I guess they consider this to be priory info and are not ready to decimate their methods. Some results seem questionable. Someone with better understanding and knowledge may want to elaborate.

Thanks.

Rethel
06-21-2017, 10:23 PM
I think those numbers might be understated excessively due to under sampling. Most studies put the R1a frequency around 15 to 17% of India's male lineages. Which would be approximately 100 mil.

So why in Wikipedia is written 28-32%??

Amerijoe
06-21-2017, 10:25 PM
I think those numbers might be understated excessively due to under sampling. Most studies put the R1a frequency around 15 to 17% of India's male lineages. Which would be approximately 100 mil.

There are several others which are a little wonky. That was why I asked for the related studies, but was given generally available info instead.

Michał
06-22-2017, 12:50 AM
Yep, it was part of the Z93 panel. Though how is not clear. It was the first SNP to appear positive, which was followed by the Y6 and downwards in batches.
BY2835 doesn't seem to be a part of the Z93 panel at YSEQ (http://www.yseq.net/product_info.php?products_id=11867) and since YFull does not use this SNP for phylogenetic analysis, we may suspect that this is either a recurrent mutation found in different haplogroups or a mutation located in an unstable (repetitive?) region.

When testing individual SNPs, YSEQ usually reports all results for known mutations located in a given region (ie. in a relatively small region covered by Sanger sequencing), so it is possible that your BY2835+ result is simply a byproduct of your Z93 panel.

parasar
06-22-2017, 03:48 AM
So why in Wikipedia is written 28-32%??

These are at best estimates.
Going by the Tamil Nadu data set of Arunkumar that had 1680 samples - http://journals.plos.org/plosone/article?id=10.1371/annotation/8663819b-5ff0-4133-b70a-2d686dfb0a44 - I would think that if R1a1 at 12.74% in Tamil Nadu, it would be range from that number to 50% in some areas of the subcontinent but would be lower in some NE Tibeto Burman areas. It is higher than TN in Lanka.

homosapien
06-23-2017, 01:54 AM
BY2835 doesn't seem to be a part of the Z93 panel at YSEQ (http://www.yseq.net/product_info.php?products_id=11867) and since YFull does not use this SNP for phylogenetic analysis, we may suspect that this is either a recurrent mutation found in different haplogroups or a mutation located in an unstable (repetitive?) region.

When testing individual SNPs, YSEQ usually reports all results for known mutations located in a given region (ie. in a relatively small region covered by Sanger sequencing), so it is possible that your BY2835+ result is simply a byproduct of your Z93 panel.

Yes, I think what you mentioned is correct.

As when I looked at the SNP's to be tested under the Z93 panel the BY2835 SNP does not appear in the list (in addition to more others which i was negative for)

But it does show up in the results section, which could be due to the reason you mentioned.

Rethel
06-23-2017, 01:28 PM
These are at best estimates.
Going by the Tamil Nadu data set of Arunkumar that had 1680 samples - http://journals.plos.org/plosone/article?id=10.1371/annotation/8663819b-5ff0-4133-b70a-2d686dfb0a44 - I would think that if R1a1 at 12.74% in Tamil Nadu, it would be range from that number to 50% in some areas of the subcontinent but would be lower in some NE Tibeto Burman areas. It is higher than TN in Lanka.

So what is the real % of hgs in whole India?

parasar
07-07-2017, 02:26 PM
So what is the real % of hgs in whole India?

My estimate would be a bit higher than 12.74%, perhaps in the 20-25% range overall.
Often tribals and isolated groups are oversampled for India and that skews the R1a number downwards. For the core Indo-Gangetic plains the number would be closer to 50%.

Rethel
07-07-2017, 04:25 PM
So shortly saying, it is not known. Unfortunatly...

parasar
07-07-2017, 05:52 PM
So shortly saying, it is not known. Unfortunatly...

No I would not say it not known, just that it is fully known, and subject to sampling issues and location.

For example from the core Indo-Gangetic plain region of the Punjab we have a number - 61.3% (68/111) going to the periphery 36.5% (38/104) in W Bengal for decent enough sample sizes. https://www.omicsonline.org/open-access/the-major-ychromosome-haplotype-xi--haplogroup-r1a-in-eurasia-2161-1041-1000150.pdf