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Japanese D2 geno 2.0 y result compare

PostPosted: Thu Dec 13, 2012 4:56 pm
by dawnland
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

Re: Japanese D2 geno 2.0 y result compare

PostPosted: Thu Dec 13, 2012 7:53 pm
by fjnj
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.

Re: Japanese D2 geno 2.0 y result compare

PostPosted: Thu Dec 13, 2012 8:00 pm
by fjnj
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.

Re: Japanese D2 geno 2.0 y result compare

PostPosted: Fri Dec 14, 2012 4:13 am
by daver
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

Re: Japanese D2 geno 2.0 y result compare

PostPosted: Sat Dec 15, 2012 7:55 pm
by dawnland
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

Re: Japanese D2 geno 2.0 y result compare

PostPosted: Sat Dec 15, 2012 8:23 pm
by dawnland
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.

Re: Japanese D2 geno 2.0 y result compare

PostPosted: Fri Mar 22, 2013 8:43 am
by Itai
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.