Japanese D2 geno 2.0 y result compare


Posts: 59
Joined: Fri Mar 16, 2012 12:14 pm
PostPosted: Thu Dec 13, 2012 4:56 pm
in Japan DNA project,two D2a1b IMS-JST022457+ kit 176409 and 78279.
http://www.familytreedna.com/public/jap ... ction=ysnp

78279 snps
CTS1034+, CTS10436+, CTS10713+, CTS10738+, CTS11085+, CTS11454+, CTS11844+, CTS12173+, CTS2080+, CTS2223+, CTS230+, CTS2447+, CTS295+, CTS3234+, CTS335+, CTS3647+, CTS3763+, CTS3914+, CTS4276+, CTS4623+, CTS4714+, CTS477+, CTS5458+, CTS5580+, CTS6010 CTS6353+, CTS6384+, CTS6891+, CTS7453+, CTS7492+, CTS7859+, CTS7951+, CTS8133+, CTS8178+, CTS8244+, CTS9096+, CTS947+, CTS9512+, CTS9548+, F1173+, F1221+, F1300+, F1327+, F1369+, F1707+, F1754+, F1831+, F1833+, F1842+, F1870+, F1882+, F2000+, F2137+, F2150+, F2177+, F2223+, F2494+, F2503+, F2546+, F2631+, F2845+, F2887+, F2932+, F3035+, F3039+, F317+, F3187+, F3225+, F3394+, F3397+, F3455+, F375+, F3948+, F3965+, F4131+, F4277+, F830+, F842+, F869+, F889+, F910+, F942+, F943+, F969 L366+, L477+, L493+, L515+, L516+, L517+, L552+, L594+, M263+, P37+, PF4208+, PF4330+, PF5061+ PF6868+, PF7392+, Z148+, Z191+, Z365+

176409 snps
CTS6055+, F4220+

common snps
CTS101+, CTS1014+, CTS1024+, CTS10362+, CTS10441+, CTS10536+, CTS10564+, CTS10646+, CTS1069+, CTS107+, CTS10714+, CTS10750+, CTS109+, CTS10933+, CTS11264+, CTS11358+, CTS11575+, CTS11577+, CTS1171+, CTS11834+, CTS12007+, CTS125+, CTS1582+, CTS1817+, CTS1821+, CTS1841+, CTS1904+, CTS1982+, CTS1996+, CTS2112+, CTS2478+, CTS2728+, CTS3177+, CTS323+, CTS3331+, CTS3334+, CTS3397+, CTS3431+, CTS3621+, CTS3651+, CTS3662+, CTS3768+, CTS3978+, CTS4364+, CTS4368+, CTS4661+, CTS4740+, CTS4913+, CTS5001+, CTS5318+, CTS5406+, CTS5457+, CTS5532+, CTS5828+, CTS5829+, , CTS6248+, CTS6332+, CTS6383+, CTS6394+, CTS642+, CTS6448+, CTS6494+, CTS6655+, CTS6800+, CTS6886+, CTS6907+, CTS6945+, CTS7089+, CTS7106+, CTS7165+, CTS7214+, CTS7471+, CTS7660+, CTS7922+, CTS7933+, CTS7962+, CTS8060+, CTS8093+, CTS8181+, CTS8210+, CTS8243+, CTS8348+, CTS8435+, CTS8484+, CTS8540+, CTS8583+, CTS8613+, CTS8880+, CTS8914+, CTS8980+, CTS9051+, CTS9061+, CTS911+, CTS9120+, CTS9246+, CTS932+, CTS94+, CTS9828+, CTS9896+, CTS9988+, F1034+, F1066+, F1137+, F1264+, F1278+, F1306+, F1344+, F1379+, F1439+, F1447+, F1533+, F1612+, F1620+, F1690+, F1927+, F1977+, F2062+, F2147+, F2161+, F2318+, F2325+, F2455+, F2473+, F2510+, F2662+, F2765+, F2923+,F2956+,F3170+, F3195+, F3289+, F3321+, F3328+, F3370+, F3519+, F3572+, F3666+, F3707+, F3835+, F3845+, F3920+, F4030+, , F974+, F975+, F986+, IMS-JST022457+, L566+, L781+, M139+, M145+,M168+, M174+, M203+, M294+, M42+, M55+, M64+, M94+, P144+, P153+, P165+, P183+, PAGES00003+, PF1016+, PF1029+, PF1031+, PF1040+, PF1046+, PF1061+, PF1092+, PF1097+, PF110+, PF1203+, PF1269+, PF1276+, PF1427+, PF1442+, PF1455+, PF15+, PF192+, PF210+, PF212+, PF223+, PF234+, PF258+, PF263+, PF272+, PF278+, PF292+, PF316+, PF325+, PF342+, PF500+, , PF601+, PF667+, PF719+, PF720+, PF725+, PF779+, PF796+, PF803+, PF815+, PF821+, PF840+, PF844+, PF892+, PF937+, PF951+, PF954+, PF970+, V189+, V52+, V9+

some snps may previous tested,but their results very different,not close.
176409 is M116-,78279 not display M116 seems also M116-
78279 has PF4208+, PF4330+, PF5061+ PF6868+, PF7392+, Z148+, Z191+, Z365,one O3 kit 199578 also has these snps
http://www.familytreedna.com/public/o3/ ... ction=ysnp

Posts: 40
Joined: Tue Jul 31, 2012 7:46 pm
PostPosted: Thu Dec 13, 2012 7:53 pm
dawnland wrote:in Japan DNA project,two D2a1b IMS-JST022457+ kit 176409 and 78279.
http://www.familytreedna.com/public/jap ... ction=ysnp

78279 snps
CTS1034+, CTS10436+, CTS10713+, CTS10738+, CTS11085+, CTS11454+, CTS11844+, CTS12173+, CTS2080+, CTS2223+, CTS230+, CTS2447+, CTS295+, CTS3234+, CTS335+, CTS3647+, CTS3763+, CTS3914+, CTS4276+, CTS4623+, CTS4714+, CTS477+, CTS5458+, CTS5580+, CTS6010 CTS6353+, CTS6384+, CTS6891+, CTS7453+, CTS7492+, CTS7859+, CTS7951+, CTS8133+, CTS8178+, CTS8244+, CTS9096+, CTS947+, CTS9512+, CTS9548+, F1173+, F1221+, F1300+, F1327+, F1369+, F1707+, F1754+, F1831+, F1833+, F1842+, F1870+, F1882+, F2000+, F2137+, F2150+, F2177+, F2223+, F2494+, F2503+, F2546+, F2631+, F2845+, F2887+, F2932+, F3035+, F3039+, F317+, F3187+, F3225+, F3394+, F3397+, F3455+, F375+, F3948+, F3965+, F4131+, F4277+, F830+, F842+, F869+, F889+, F910+, F942+, F943+, F969 L366+, L477+, L493+, L515+, L516+, L517+, L552+, L594+, M263+, P37+, PF4208+, PF4330+, PF5061+ PF6868+, PF7392+, Z148+, Z191+, Z365+

176409 snps
CTS6055+, F4220+

common snps
CTS101+, CTS1014+, CTS1024+, CTS10362+, CTS10441+, CTS10536+, CTS10564+, CTS10646+, CTS1069+, CTS107+, CTS10714+, CTS10750+, CTS109+, CTS10933+, CTS11264+, CTS11358+, CTS11575+, CTS11577+, CTS1171+, CTS11834+, CTS12007+, CTS125+, CTS1582+, CTS1817+, CTS1821+, CTS1841+, CTS1904+, CTS1982+, CTS1996+, CTS2112+, CTS2478+, CTS2728+, CTS3177+, CTS323+, CTS3331+, CTS3334+, CTS3397+, CTS3431+, CTS3621+, CTS3651+, CTS3662+, CTS3768+, CTS3978+, CTS4364+, CTS4368+, CTS4661+, CTS4740+, CTS4913+, CTS5001+, CTS5318+, CTS5406+, CTS5457+, CTS5532+, CTS5828+, CTS5829+, , CTS6248+, CTS6332+, CTS6383+, CTS6394+, CTS642+, CTS6448+, CTS6494+, CTS6655+, CTS6800+, CTS6886+, CTS6907+, CTS6945+, CTS7089+, CTS7106+, CTS7165+, CTS7214+, CTS7471+, CTS7660+, CTS7922+, CTS7933+, CTS7962+, CTS8060+, CTS8093+, CTS8181+, CTS8210+, CTS8243+, CTS8348+, CTS8435+, CTS8484+, CTS8540+, CTS8583+, CTS8613+, CTS8880+, CTS8914+, CTS8980+, CTS9051+, CTS9061+, CTS911+, CTS9120+, CTS9246+, CTS932+, CTS94+, CTS9828+, CTS9896+, CTS9988+, F1034+, F1066+, F1137+, F1264+, F1278+, F1306+, F1344+, F1379+, F1439+, F1447+, F1533+, F1612+, F1620+, F1690+, F1927+, F1977+, F2062+, F2147+, F2161+, F2318+, F2325+, F2455+, F2473+, F2510+, F2662+, F2765+, F2923+,F2956+,F3170+, F3195+, F3289+, F3321+, F3328+, F3370+, F3519+, F3572+, F3666+, F3707+, F3835+, F3845+, F3920+, F4030+, , F974+, F975+, F986+, IMS-JST022457+, L566+, L781+, M139+, M145+,M168+, M174+, M203+, M294+, M42+, M55+, M64+, M94+, P144+, P153+, P165+, P183+, PAGES00003+, PF1016+, PF1029+, PF1031+, PF1040+, PF1046+, PF1061+, PF1092+, PF1097+, PF110+, PF1203+, PF1269+, PF1276+, PF1427+, PF1442+, PF1455+, PF15+, PF192+, PF210+, PF212+, PF223+, PF234+, PF258+, PF263+, PF272+, PF278+, PF292+, PF316+, PF325+, PF342+, PF500+, , PF601+, PF667+, PF719+, PF720+, PF725+, PF779+, PF796+, PF803+, PF815+, PF821+, PF840+, PF844+, PF892+, PF937+, PF951+, PF954+, PF970+, V189+, V52+, V9+

some snps may previous tested,but their results very different,not close.
176409 is M116-,78279 not display M116 seems also M116-
78279 has PF4208+, PF4330+, PF5061+ PF6868+, PF7392+, Z148+, Z191+, Z365,one O3 kit 199578 also has these snps
http://www.familytreedna.com/public/o3/ ... ction=ysnp

One is a lot cleaner than the other with far fewer false positives.

Posts: 40
Joined: Tue Jul 31, 2012 7:46 pm
PostPosted: Thu Dec 13, 2012 8:00 pm
These F-snps are problematic:
F1173, F1221, F1300, F1369, F1707, F1754, F1831, F1833, F1842, F1882, F2000, F2137, F2150, F2177, F2223, F2494, F2503, F2546, F2631, F2845, F2887, F2932, F3035, F3039, F317, F3187, F3225, F3394, F3397, F3455, F3566, F375, F3948, F3965, F4131, F4277, F830, F842, F869, F889, F910, F942, F943, F969

They are all reported in individuals from unrelated haplogroups, which suggest either contamination or independent mutations.
User avatar
Posts: 71
Joined: Tue Jun 12, 2012 5:57 pm

YDNA:
R-L627
PostPosted: Fri Dec 14, 2012 4:13 am
Any chance of getting copies of the results files for either or both (not for publication or further distribution would be OK)?

I'm trying to compare as many haplogroups as I can to verify validity of backbone SNPs as well as identify problem SNPs.

Regards,
david
geno (at) daver.info

Posts: 59
Joined: Fri Mar 16, 2012 12:14 pm
PostPosted: Sat Dec 15, 2012 7:55 pm
fjnj wrote:These F-snps are problematic:
F1173, F1221, F1300, F1369, F1707, F1754, F1831, F1833, F1842, F1882, F2000, F2137, F2150, F2177, F2223, F2494, F2503, F2546, F2631, F2845, F2887, F2932, F3035, F3039, F317, F3187, F3225, F3394, F3397, F3455, F3566, F375, F3948, F3965, F4131, F4277, F830, F842, F869, F889, F910, F942, F943, F969

They are all reported in individuals from unrelated haplogroups, which suggest either contamination or independent mutations.

yes plus F1327 and F1870.F3566 is found at 2 O and 2 N,no obvious abnormality so far,it may derived form NO
problems snps:
CTS1034,CTS10436,CTS10713,CTS10738,CTS11085,CTS11454,CTS11844,CTS12173,CTS2080,CTS2223,CTS230,CTS2447,CTS295,CTS3234,CTS335,CTS3647,CTS3763CTS3914,CTS4276,CTS4623,CTS4714, CTS477,CTS5458,CTS5580,CTS6010,CTS6353, CTS6384,CTS6891CTS7453,CTS7492,CTS7859,CTS7951,CTS8133, CTS8178, CTS8244,CTS9096, CTS947, CTS9512,CTS9548, F1173, F1221, F1300,F1327,F1369, F1707, F1754,F1831, F1833, F1842, F1870, F1882, F2000, F2137,F2150, F2177,F2223,F2494, F2503, F2546, F2631,F2845, F2887,F2932, F3035, F3039, F317, F3187,F3225 F3394, F3397,F3455,F375, F3948, F3965, F4131, F4277, F830, F842, F869, F889, F910,F942, F943, F969,L366,L477, L493,L515, L516, L517,L552, L594, M263, PF4208, PF4330, PF5061, PF6868,PF7392 Z148, Z191, Z365

Posts: 59
Joined: Fri Mar 16, 2012 12:14 pm
PostPosted: Sat Dec 15, 2012 8:23 pm
so removed problem snps,78279 not has additional snp

F115-> CTS1014-> CTS2728-> CTS6055 =CTS1024
78279 is CTS1024+,CTS6055 maybe no call.F4220 maybe no call too.these two D2 maybe snp result same.

Posts: 10
Joined: Wed Sep 26, 2012 12:46 pm

YDNA:
G-L91
MtDNA:
K1a9
PostPosted: Fri Mar 22, 2013 8:43 am
There are three results now. I am working on a comparative file on excel. As soon as I finish it, I'll post you a link.

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