I think we have to call Dr. Chuanchao @wang for help:)

Hi thanks for reporting the bug.
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Could you possibly give me more information about your haplogroup that 23andme generates for you since we use a different version of Y tree to name the lineage, which is confusing sometimes?
Could you show the paternal lineage tree following the steps here to check if there are mutations really matched on this particular J2 haplogroup??
http://www.sofreetech.com/question/1559

Thanks for the prompt reply! Below (attached as figures) are the corresponding results provided by 23andMe and WeGene.




Result from 23andMe
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Result from WeGene
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To confirm this haplogroup assignment, I tried some third party programs previously, such as yhaplo,?and they all gave me the same result.

I also checked some SNPs by myself and they all look about right. The major ones are listed as follows.
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SNP ? ?rsid ? ?chromosome ? ?position ? ?genotype
M304/Page16/PF4609 ? ?rs13447352 ? ?Y ? ?22749853 ? ?C
CTS5628/PF4555 ? ?rs17307231 ? ?Y ? ?16401405 ? ?G
P209/PF4584 ? ?rs17315835 ? ?Y ? ?19179335 ? ?C
CTS5280/PF4550 ? ?rs17307175 ? ?Y ? ?16180103 ? ?G
F2502/PF4564 ? ?rs17222412 ? ?Y ? ?17495914 ? ?A
M172/Page28/PF4908 ? ?rs2032604 ? ?Y ? ?14969634 ? ?G
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So I guess the inference of my general paternal haplogroup should be correct, but there may be some issues with the front-end visualization on WeGene. I can share my 23andMe raw data with you if you want.
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Thanks,
J

thanks for posting.the haplogroup?assignments are consistent in suggesting you belong to J. I agree with you that the problem is front-end visualization but not our scientific interpretation. I will contact our IT department to figure out what happened to the visual. Thanks.?

I just get the feedback that we have not included haplogroup J into our visualizations because this lineage is so rare in Chinese. We will update our system to also add those rare haplogroups into it.Thanks!?

Thanks for the confirmation! Glad that I can contribute a little to the further improvement of this good platform.
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As you mentioned that the haplogroup J2 is very rare among Han Chinese populations, I'm quite curious about its putative migration routes and history in China, and how did this presumably Middle East originated Y chromosome haplogroup/gene pool introgressed into Han Chinese population. From the limited amount of publications I could find about the distribution of this haplogroup among the populations (especially Han Chinese populations) in China/East Asia, it seems that this haplogroup constitute a significant proportion of some minority populations from Northwest China (including Uyghurs, Uzbeks, Tajiks, Hui, etc.), but a fairly low (1-5%) though pretty homogenized distribution among the Han Chinese populations from several Northwest provinces (Xinjiang, Qinghai, Gansu, Ningxia, etc.). I guess one of the plausible hypothesis would be that there were small but constant migration flows from the central Asia populations to Northwest China long before the Islamic expansions, though I'm not sure whether this hypothesis is consistent with the fact that this haplogroup is even much rarer (if any) in other Han Chinese populations that are more Southeastern, considering that they had inhabited Gansu and Shaanxi that long ago.

It would be great if I could learn more about this from expert like you.
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best,
J

I am sharing with you a paper explaining the present-day fragmented distribution of West Eurasian lineages in China:
http://mbe.oxfordjournals.org/content/28/1/717.short
Zhong H, Shi H, Qi XB, Duan ZY, Tan PP, Jin L, Su B, Ma RZ. Extended Y chromosome investigation suggests postglacial migrations of modern humans into East Asia via the northern route. Molecular biology and evolution. 2011 Jan 1;28(1):717-27.