Nat Geo 2.0 Next Gen Y-DNA haplogroup prediction seems wrong

[ddxue]

My Y-DNA haplogroup came out as J-CTS2906, which seems to be also known as J2-M92 or J2a1b1. The problem is... I'm Han Chinese from Eastern China and I couldn't find any studies that found J2 in Han Chinese (or J1 for that matter). My autosomal breakdown on gedmatch using the various admixture tools is ~70-90% East Asian and ~10-30% Siberian. The gedmatch oracle consistently lists Northern Han Chinese and various Tibeto-Burman speaking minorities as the populations with the shortest genetic distance from me.

The FTDNA transfer results are a mess. It only lists SNP's I tested positive for, not the ones I tested negative for. I used the ISOGG tree chrome extension to view them and there are positive matches in many haplogroups. On a quick glance it seems I have the most in haplogroup I1 and J2 (isn't I1 Scandinavian?). Here are my FTDNA Y-DNA SNP transfer results:

A531+, A91+, BY1142+, BY1357+, BY136_FGC19909_Z18229+, BY1551+, BY1586+, BY1734+, BY20+, BY2243+, BY2391+, BY2462+, BY2510+, BY65_Z18181+, BY763+, BY876+, CTS10031+, CTS10147+, CTS10188+, CTS10229+, CTS103+, CTS10300+, CTS10428+, CTS10433+, CTS10442+, CTS10448+, CTS10534+, CTS10552+, CTS10572+, CTS10615+, CTS10648+, CTS1066+, CTS10720+, CTS10723+, CTS10745+, CTS10761+, CTS10821+, CTS1083+, CTS10847+, CTS10923+, CTS11012+, CTS11041+, CTS11071+, CTS11088+, CTS11126+, CTS11148+, CTS11149+, CTS11190+, CTS11261+, CTS11354+, CTS114+, CTS1141+, CTS11436+, CTS11441+, CTS1148+, CTS11503+, CTS11522+, CTS11530+, CTS11544+, CTS1164+, CTS11651+, CTS1171+, CTS11710+, CTS11726+, CTS11731+, CTS11759+, CTS11816+, CTS11907+, CTS11949+, CTS11970+, CTS12023+, CTS12058+, CTS1216+, CTS12449+, CTS12450+, CTS12472+, CTS12578+, CTS12652+, CTS1276+, CTS12856+, CTS12879+, CTS12931+, CTS12933+, CTS12934+, CTS12948+, CTS12976+, CTS1340+, CTS1353+, CTS1413+, CTS1436+, CTS1633+, CTS1710+, CTS1758+, CTS1806+, CTS1831+, CTS1854+, CTS191+, CTS2+, CTS202+, CTS2067+, CTS210+, CTS2105+, CTS2134+, CTS2230+, CTS2275+, CTS2284+, CTS2289+, CTS2413+, CTS244+, CTS2488+, CTS2491+, CTS2515+, CTS2550+, CTS2670+, CTS2709+, CTS278+, CTS280+, CTS2800+, CTS2848+, CTS2906+, CTS2947+, CTS305+, CTS316+, CTS3202+, CTS3221+, CTS3268+, CTS3366+, CTS3403+, CTS3430+, CTS3466+, CTS347+, CTS3519+, CTS352+, CTS3536+, CTS3543+, CTS3654+, CTS3658+, CTS3663+, CTS3700+, CTS3802+, CTS3837+, CTS3868+, CTS3902+, CTS3996+, CTS4053+, CTS4086+, CTS4089+, CTS4094+, CTS4137+, CTS4178+, CTS4209+, CTS4235+, CTS4326+, CTS4406+, CTS4443+, CTS4463+, CTS4608+, CTS4643+, CTS4715+, CTS4781+, CTS4784+, CTS4793+, CTS4853+, CTS4984+, CTS5052+, CTS5152+, CTS5156+, CTS5254+, CTS5304+, CTS5334+, CTS5359+, CTS5370+, CTS5383+, CTS5410+, CTS5522+, CTS5649+, CTS5690+, CTS58+, CTS5828+, CTS585+, CTS5860+, CTS5874+, CTS5933+, CTS5939+, CTS597+, CTS5998+, CTS6062+, CTS6063+, CTS6090+, CTS6117+, CTS6135+, CTS6265+, CTS6266+, CTS6285+, CTS6352+, CTS636+, CTS6365+, CTS6378+, CTS6394+, CTS6403+, CTS6438+, CTS6447+, CTS6449+, CTS6468+, CTS6481+, CTS6492+, CTS6506+, CTS656+, CTS6613+, CTS6631+, CTS6677+, CTS6704+, CTS6848+, CTS6865+, CTS687+, CTS6916+, CTS6918+, CTS6967+, CTS7022+, CTS7101+, CTS7120+, CTS7147+, CTS7167+, CTS7186+, CTS7193+, CTS7227+, CTS7266+, CTS7275+, CTS7285+, CTS7299+, CTS730+, CTS7317+, CTS7335+, CTS736+, CTS7451+, CTS7598+, CTS7601+, CTS7611+, CTS7626+, CTS7642+, CTS7803+, CTS7810+, CTS7925+, CTS7929+, CTS7942+, CTS8027+, CTS8126+, CTS8203+, CTS8216+, CTS8300+, CTS8301+, CTS8440+, CTS8492+, CTS8506+, CTS8521+, CTS860+, CTS8645+, CTS8723+, CTS8815+, CTS8889+, CTS9056+, CTS914+, CTS9154+, CTS9240+, CTS9322+, CTS9325+, CTS9335+, CTS9387+, CTS9471+, CTS9518+, CTS9525+, CTS9539+, CTS9558+, CTS9677+, CTS97+, CTS9716+, CTS9757+, CTS9894+, CTS9900+, CTS9925+, CTS9975+, CTS9976+, DF109_FGC4101_S660_Y2845+, F1007+, F1012+, F1013+, F1024+, F1030+, F1055+, F1096+, F1108+, F1127+, F1159+, F1191+, F1207+, F1217+, F1221+, F1241+, F1291+, F1302+, F1307+, F1329+, F1367+, F1382+, F1405+, F1412+, F142+, F1420+, F1442+, F1474+, F1476+, F1490+, F1539+, F1540+, F1564+, F1567+, F1574+, F1594+, F1597+, F1677+, F1703+, F1704+, F1712+, F1714+, F1727+, F1753+, F1767+, F1796+, F1804+, F1813+, F1848+, F1874+, F188+, F1899+, F1905+, F1924+, F1946+, F1956+, F2018+, F202+, F2028+, F2048+, F2067+, F2132+, F2142+, F2149+, F2155+, F2165+, F2208+, F2211+, F2224+, F2236+, F2282+, F2304+, F2327+, F2332+, F2343+, F2370+, F2371+, F2379+, F240+, F2402+, F2434+, F2480+, F2512+, F2516+, F2546+, F2558+, F2587+, F2600+, F2620+, F2654+, F2673+, F2688+, F2710+, F2718+, F2724+, F2742+, F2753+, F2761+, F2767+, F2792+, F2808+, F2837+, F2840+, F2850+, F2869+, F287+, F2873+, F2924+, F2947+, F2960+, F2961+, F2985+, F299+, F2990+, F2992+, F3032+, F3043+, F3048+, F3056+, F3057+, F3082+, F3108+, F3111+, F3122+, F3136+, F3143+, F3195_PF1806+, F3270+, F3311+, F3324+, F3335+, F3368_PF3566+, F3395+, F3402_PF3567+, F3422+, F3444+, F3451+, F3491+, F3518+, F3556+, F3582+, F3595+, F3625+, F3632+, F3643+, F3670+, F3692+, F3697+, F371+, F3735+, F3739+, F3744+, F3789+, F3806+, F386+, F3869+, F3892+, F3907+, F3949+, F3956+, F3994+, F3998+, F4003+, F4010+, F4111+, F4176+, F4188_PF3539+, F4244+, F4251+, F4257+, F4282+, F4338+, F492+, F526+, F557+, F565+, F61+, F646+, F716+, F719+, F736+, F741+, F743+, F767+, F771+, F819+, F836+, F837+, F845+, F862+, F896+, F910+, F995+, FGC11678+, FGC11897_YP327+, FGC16179_Y6682_Z4084+, FGC16192_Y4462_Z16217+, FGC16362_Z18162+, FGC16466_Z16739+, FGC16683_Y5619+, FGC1721_Y5322+, FGC20866_ZS2566+, FGC20874_ZS2572+, FGC24646+, FGC28639_YP556+, FGC29572+, FGC3718_Y6369+, FGC6948_Y2703+, IMS-JST029149+, K257+, K386+, L104+, L1093+, L1186+, L1247+, L132+, L1324+, L167+, L183+, L187+, L213+, L245+, L253+, L254+, L294+, L325+, L387+, L440+, L442+, L453+, L459+, L464_1+, L484+, L492+, L496+, L498+, L503+, L533+, L542+, L551+, L552+, L556+, L557+, L625+, L636+, L665+, L72+, L782+, L784+, L817+, L840+, L99+, M102+, M116+, M129+, M139+, M171+, M251+, M262+, M275+, M288+, M367+, M39+, M94+, M9574+, M9588+, MC14+, N4+, NGC5+, P102+, P108+, P117+, P118+, P129+, P135+, P136+, P141+, P145+, P148+, P151+, P159+, P160+, P166+, P181+, P194+, P202+, P268+, P269+, P289+, P305+, P40+, P52+, P59+, P77+, P80+, P84+, P91+, PAGES00010+, PAGES00048+, PAGES00081+, PAGES00101+, PAGES00105+, PF1015+, PF1026+, PF1031+, PF1085+, PF1097+, PF1141+, PF1147+, PF1152+, PF1164+, PF1169+, PF121+, PF1226+, PF1232+, PF1252+, PF1269+, PF1270+, PF1279+, PF1283+, PF133+, PF1368+, PF147+, PF156+, PF1562+, PF1577+, PF1587+, PF22+, PF228+, PF2334+, PF2436+, PF2438+, PF2466+, PF2481+, PF2495+, PF2579+, PF2593+, PF2611+, PF2624+, PF2635+, PF2643+, PF2745+, PF276+, PF288+, PF293+, PF302+, PF3051+, PF3086+, PF3107+, PF3188+, PF3220+, PF3248+, PF328+, PF3298+, PF331+, PF3320+, PF3561+, PF3823+, PF3890+, PF3964+, PF3986+, PF40+, PF4105+, PF4193+, PF4246+, PF4533+, PF4573+, PF4576+, PF4589+, PF4592+, PF4647+, PF4653+, PF4720+, PF4876+, PF4879+, PF4888+, PF4957+, PF5014+, PF5104+, PF5122+, PF5123+, PF5125+, PF5147+, PF5169+, PF535+, PF5381+, PF5436+, PF5517+, PF5735+, PF5744+, PF5784+, PF5787+, PF5792+, PF5815+, PF5819+, PF601+, PF6063+, PF625+, PF6275+, PF6286+, PF6300+, PF6314+, PF6369+, PF644+, PF6673+, PF668+, PF671+, PF679+, PF6864+, PF6865+, PF6914+, PF698+, PF700+, PF7067+, PF7328+, PF7341+, PF7374+, PF7434+, PF747+, PF7527+, PF7552+, PF7557+, PF791+, PF794+, PF806+, PF829+, PF888+, PF907+, PF926+, PF93+, PF946+, PF95+, PF966+, PF968+, PF971+, PF997+, PK1+, PR805+, rs35407486+, rs9785743+, rs9786774+, S3207+, s5153+, S7123+, SK1247_Y4915+, SK1410_Y5528_Z20169+, V174+, V183_F1743+, V186+, V187+, V199+, V205+, V21+, V216+, V221+, V227+, V232_F1029+, V250+, V29+, V32+, V59+, V78+, V79+, V8+, V90+, V94+, Y1038+, Y1049+, Y1083+, Y1113+, Y1122+, Y2799_Z7648+, Y32+, Y4482_Z12144+, Y4486_Z4016+, Y4488_Z4051+, Y4493_Z4133+, Y4496_Z7169+, Y4864_Z16422+, Y5272+, Y5305_Z16500+, Y5759_Z16420+, Y6181+, Y6674_Z3968+, Y6691+, Y6694_Z4141+, Y763+, YP321+, YSC0000081+, YSC0000150+, YSC0000216+, YSC0000292+, YSC0001071+, Z11180+, Z1149+, Z12163+, Z12214+, Z130+, Z133+, Z138+, Z1435+, Z1455+, Z1456+, Z1459+, Z1476+, Z148+, Z1483+, Z1504+, Z1518+, Z1589+, Z1593+, Z1616+, Z18133+, Z18140+, Z1817+, Z18186+, Z1835+, Z187+, Z189+, Z1975+, Z2069+, Z2082+, Z2094+, Z213+, Z2396+, Z269+, Z270+, Z274+, Z284+, Z2970+, Z2976+, Z2983+, Z30+, Z306+, Z315+, Z319+, Z347+, Z350+, Z3723+, Z39+, Z3965+, Z3999+, Z4059+, Z4073+, Z4083+, Z4090+, Z4091+, Z4095+, Z4145+, Z4151+, Z477+, Z515+, Z531+, Z544+, Z60+, Z625+, Z638+, Z72+, Z75+, Z767+, Z966+, ZS1727+, ZS251+

Is there any way to get to the bottom of this without paying for additional Y-DNA testing?

[Parameswara]

Y-DNA has nothing to do with autosomal. You could be 100% east asian with any Y-DNA haplogroup. If you have non-chinese patrilineal ancestor, within 8-10 generation his non-chinese autosomal could be diluted.

[Parameswara]

Haplogroup J

[Parameswara]

Henan J2

[Kavellion]

J2 most commonly associated as jewish or arab, middle eastern anyway. I would think that a result like this for someone who was in another population would be pretty neat for the tester. All sorts of people were going to China to trade in the past.

[Armando]

My Y-DNA haplogroup came out as J-CTS2906, which seems to be also known as J2-M92 or J2a1b1. The problem is... I'm Han Chinese from Eastern China and I couldn't find any studies that found J2 in Han Chinese (or J1 for that matter). My autosomal breakdown on gedmatch using the various admixture tools is ~70-90% East Asian and ~10-30% Siberian. The gedmatch oracle consistently lists Northern Han Chinese and various Tibeto-Burman speaking minorities as the populations with the shortest genetic distance from me.

The FTDNA transfer results are a mess. It only lists SNP's I tested positive for, not the ones I tested negative for. I used the ISOGG tree chrome extension to view them and there are positive matches in many haplogroups. On a quick glance it seems I have the most in haplogroup I1 and J2 (isn't I1 Scandinavian?). Here are my FTDNA Y-DNA SNP transfer results:



Is there any way to get to the bottom of this without paying for additional Y-DNA testing?

Geno 2.0 NextGen is a real mess which is why you are seeing a mess at FTDNA. You are in haplogroup C. You match on almost all of your SNPs with the person whose father tested positive for C-M217 at 23andme and also has the STR haplotype of C-M217 at FTDNA.

[ddxue]

One of the project Haplogroup C administrators responded to me and gave me a document with SNP's I should check for. I test positive for a lot of the general C-M130 SNP's in that document. These were in the ISOGG 2016 tree for haplogroup C but weren't in the 2015 tree so they weren't highlighted for me (bug with Chrome extension maybe?).

I have positive SNP's in a few different subclades of C:

C1a1 - CTS7285
C1b1a2b - F736, F741
C2e1a - F3949
C2e1a1 - F3739
C2e1b1a - F3735, F3806
C2e2 - F845, CTS6704, CTS10923, CTS12931

Unfortunately, I also test positive for a lot of the general J-M304 SNP's (seems like the ISOGG 2016 tree for haplogroup J is the same as the 2015 tree). These are the subclades of haplogroup J I have positive SNP's in:

J1a2b3 - L817
J2a1b1a - L556
J2a1h2c - L254
J2b - M102

I also test positive for a lot of SNP's in haplogroup I. This is just a huge mess.

Haplogroup C: https://docs.google.com/document/d/1...Pna4uvBELWRwU/

Haplogroup J: https://docs.google.com/document/d/1...fxNWs_9_UNPlw/

[dna]

@ddxue, it is not a mess.

It is just that the same SNP can occur at different branches. We knew that about some of them, but with Big Y (and other research) more such situations are being discovered.

Mr W

P.S.
Feel the bleeding edge of scientific research

[Armando]

One of the project Haplogroup C administrators responded to me and gave me a document with SNP's I should check for. I test positive for a lot of the general C-M130 SNP's in that document. These were in the ISOGG 2016 tree for haplogroup C but weren't in the 2015 tree so they weren't highlighted for me (bug with Chrome extension maybe?).

I have positive SNP's in a few different subclades of C:

C1a1 - CTS7285
C1b1a2b - F736, F741
C2e1a - F3949
C2e1a1 - F3739
C2e1b1a - F3735, F3806
C2e2 - F845, CTS6704, CTS10923, CTS12931

Unfortunately, I also test positive for a lot of the general J-M304 SNP's (seems like the ISOGG 2016 tree for haplogroup J is the same as the 2015 tree). These are the subclades of haplogroup J I have positive SNP's in:

J1a2b3 - L817
J2a1b1a - L556
J2a1h2c - L254
J2b - M102

I also test positive for a lot of SNP's in haplogroup I. This is just a huge mess.

Haplogroup C: https://docs.google.com/document/d/1...Pna4uvBELWRwU/

Haplogroup J: https://docs.google.com/document/d/1...fxNWs_9_UNPlw/

This goes to show how bad of a job Geno 2.0 NextGen is doing for some people.

[Armando]

@ddxue, it is not a mess.

It is just that the same SNP can occur at different branches. We knew that about some of them, but with Big Y (and other research) more such situations are being discovered.

Mr W

P.S.
Feel the bleeding edge of scientific research

It's a mess because Geno 2.0 NextGen put his terminal SNP as J-CTS2906. He is the 2nd haplogroup C person to have this problem. BigY testing doesn't put people in the wrong haplogroup.

[ddxue]

After much help from Ray Banks, the administrator of the haplogroup C ISOGG tree, I'm sure I'm not haplogroup J. From the haplogroup J google doc, I searched every SNP that defines J-M304 (the top-level mutation). Many SNP's were not tested and were not in the csv file with my raw SNP results. However, many were in the file and I quickly came across many SNP's that I did not have the mutation for. Therefore there is no way I can be haplogroup J.

Then I looked at the haplogroup C google doc and looked up the SNP's that define C-M130. Nat Geo tested 13 of the SNP's that define C-M130 and I test positive for the mutation on 12 of them. I'm unclear as to why I do not have the F1367 C->G mutation since Ray told me if I am haplogroup C I should have ALL of the M130 mutations that were tested for.

Right now I'm operating the assumption I'm haplogroup C. It looks like I'm in C2/C-M217. I'm currently trying to figure out what specific subclade I belong to (if it's even possible with the level of testing Nat Geo did).

[Parameswara]

I don't know if you can download the data from Geno 2.0 Next Generation or not because I can download the data from my Geno 2.0 and see the result of those SNPs.

Then I suggest you to get Y-STR test to see the STR values. Or you can skip it and test some SNP (in FTDNA or YSEQ). And if you can afford it, then you can order NGS test like Big Y from FTDNA, or Y Elite 2.1 from FGC.

[ddxue]

I think my subclade is C2e1b F845. Looks like I experienced the exact same thing as the other guy on anthrogenica forums who was mis-classified as J-CTS2906 by Nat Geo Next Gen (he also ended up in C2e1b F845 subclade).

The results of my research:

Haplogroup C (C-M103):
CTS3221+
CTS6266+
CTS11544+
F1030+
F1217+
F1241+
F1307+
F1367- I lack this C->G mutation - I have C
F1727+
F2792+
F3043+
F3395+
V199+

Haplogroup C2 (C-M217):
CTS244+
CTS1831+
CTS3430+
CTS5410+
CTS6865+
CTS9677+
F1574+
F1597+
F1677+
F2379+
F2512+
F2718+
F3122+
F3324+
F3643+
F4010+
Z12163- I lack this A->T mutation - I have A

C2e1b:
F845+
CTS6704+
CTS12931+
CTS2123- I lack this G->T mutation - I have G
CTS11522+

I was unable to see if I'm C2e1b1 or C2e1b4 since Nat Geo didn't test the SNP's that define those subclades. However, I know I'm not C2e1b2 or C2e1b3 since I did not test positive for the SNP's that define those subclades.

Much thanks to Ray Banks, the admin of the haplogroup C project and the haplogroup C ISOGG tree for his help.

[Armando]

I don't know if you can download the data from Geno 2.0 Next Generation or not because I can download the data from my Geno 2.0 and see the result of those SNPs.

Geno 2.0 NextGen customers have to do a transfer to FTDNA to be able to download the CSV file that has the alleles of the 13,600 or so SNPs they were tested for. Whenever a person has a list of positive SNPs from Geno 2.0 NextGen it means that they have already done the transfer so all they have to do is look for the CSV file. That is how a person can find out if they were tested for certain SNPs or not.

[Armando]

I was unable to see if I'm C2e1b1 or C2e1b4 since Nat Geo didn't test the SNP's that define those subclades. However, I know I'm not C2e1b2 or C2e1b3 since I did not test positive for the SNP's that define those subclades.

Are you sure that you don't have F1673 in your CSV file? It shows up in the CSV file of other people that had the Geno 2.0 NextGen test and it is one of the SNPs that define C2e1b1.

Are there more than 13,000 SNPs in the file that you are looking at? If not, then you don't have the right file.