Information on the East Asian - Japanese Metapopulation

The Japanese Metapopulation (East Asian - Japanese) consists of 2,303 haplotypes (at least minimal) which were published in 7 population studies and were additionally submitted via personal communication (1 submission) .

Most common haplotypes

Count	DYS19	DYS389I	DYS389II	DYS390	DYS391	DYS392	DYS393	DYS385
76	17	14	31	25	10	11	13	13,17
74	15	14	30	22	10	13	13	10,20
52	15	14	30	22	10	13	13	10,19
34	15	13	30	25	10	11	13	14,17
32	15	14	29	22	10	13	13	10,20
32	15	14	30	22	10	13	13	10,18
28	15	14	29	22	10	13	13	10,19
25	16	14	31	25	10	11	13	13,17
22	13	13	29	24	10	11	14	13,15
21	16	14	29	23	10	13	13	10,18

Count	DYS391	DYS389I	DYS439	DYS389II	DYS438	DYS437	DYS19	DYS392	DYS393	DYS390	DYS385
48	10	14	12	31	10	14	17	11	13	25	13,17
36	10	14	12	30	13	14	15	13	13	22	10,20
27	10	14	12	30	13	14	15	13	13	22	10,19
25	10	13	12	30	10	14	15	11	13	25	14,17
21	10	14	12	30	13	14	15	13	13	22	10,18
15	10	14	12	29	13	14	15	13	13	22	10,19
15	10	14	12	31	10	14	16	11	13	25	13,17
14	10	14	13	30	13	14	15	13	13	22	10,19
13	10	14	12	29	13	14	16	13	13	23	10,18
12	10	14	12	29	13	14	15	13	13	22	10,20

Count	DYS456	DYS389I	DYS390	DYS389II	DYS458	DYS19	DYS385	DYS393	DYS391	DYS439	DYS635	DYS392	YGATAH4	DYS437	DYS438	DYS448
32	15	14	25	31	15	17	13,17	13	10	12	21	11	11	14	10	19
13	15	14	22	30	17	15	10,20	13	10	12	20	13	12	14	13	18
12	16	13	25	30	15	15	14,17	13	10	12	21	11	12	14	10	17
11	15	14	25	31	15	16	13,17	13	10	12	21	11	11	14	10	19
8	15	14	22	30	17	15	10,19	13	10	12	20	13	12	14	13	18
8	15	14	25	31	15	17	14,17	13	10	12	21	11	11	14	10	19
7	15	14	22	30	18	15	10,19	13	10	12	20	13	12	14	13	18
7	15	14	22	30	19	15	10,18	13	10	12	20	13	12	14	13	18
7	15	14	25	31	15	16	14,17	13	10	12	21	11	11	14	10	19
6	15	14	22	30	18	15	10,19	13	10	13	20	13	12	14	13	18

Count	DYS576	DYS389I	DYS448	DYS389II	DYS19	DYS391	DYS481	DYS549	DYS533	DYS438	DYS437	DYS570	DYS635	DYS390	DYS439	DYS392	DYS643	DYS393	DYS458	DYS385	DYS456	YGATAH4
2	18	14	17	31	16	10	25	13	12	10	14	17	21	27	14	11	13	13	16	12,16	16	12
2	19	14	19	31	16	10	26	12	12	10	14	18	21	25	12	11	12	13	15	13,17	15	11

Count	DYS576	DYS389I	DYS635	DYS389II	DYS627	DYS460	DYS458	DYS19	YGATAH4	DYS448	DYS391	DYS456	DYS390	DYS438	DYS392	DYS518	DYS570	DYS437	DYS385	DYS449	DYS393	DYS439	DYS481	DYF387S1	DYS533
3	19	14	21	31	22	11	15	17	11	19	10	15	25	10	11	37	17	14	13,17	31	13	12	26	37,37	12
2	18	14	21	31	21	11	15	17	11	19	10	15	25	10	11	37	17	14	13,17	31	13	12	26	37,37	12
2	19	14	22	30	21	11	16	16	12	17	10	17	25	10	11	38	18	14	13,16	33	13	12	29	34,35	12
2	20	12	22	29	20	10	18	16	12	18	10	14	25	10	13	37	18	14	18,19	32	12	11	23	36,39	11

There are no Ymax haplotypes or all haplotypes are singletons.

Discrete-Laplace frequency estimation (Minimal)

Release: R69
Loci included: DYS19, DYS389I, DYS389II^*, DYS390, DYS391, DYS392, DYS393
Central haplotypes: 22
EM converged: true
EM iterations: 18
GLM method: internal_coef
Init method: pam
Threshold frequency: 1 in 102,539
Per locus details: DL centers distribution (download PDF)

Table of haplotype centers (click to show/hide)

	DYS19	DYS389I	DYS389II^*	DYS390	DYS391	DYS392	DYS393
1	16	13	16	23	10	11	14
2	15	14	16	22	10	13	13
3	14	12	16	24	10	14	12
4	16	12	17	24	10	13	12
5	16	14	17	25	10	11	13
6	16	14	15	23	10	13	13
7	15	13	16	24	10	13	12
8	15	12	16	23	10	12	12
9	15	14	17	25	10	11	13
10	17	13	17	25	10	11	13
11	15	14	16	23	10	11	15
12	15	14	15	22	10	13	13
13	17	14	17	25	10	11	13
14	15	13	17	25	10	11	13
15	13	13	16	24	10	11	14
16	14	13	16	23	10	14	13
17	15	13	16	22	10	13	13
18	17	12	16	25	10	13	12
19	16	11	16	23	11	12	12
20	15	12	17	24	10	14	14
21	15	13	15	22	10	13	13
22	15	14	18	23	10	12	12

Discrete-Laplace frequency estimation (Y17)

Release: R69
Loci included: DYS19, DYS389I, DYS389II^*, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATAH4
Central haplotypes: 25
EM converged: true
EM iterations: 88
GLM method: internal_coef
Init method: pam
Threshold frequency: 1 in 48,839,834
Per locus details: DL centers distribution (download PDF)

Table of haplotype centers (click to show/hide)

	DYS19	DYS389I	DYS389II^*	DYS390	DYS391	DYS392	DYS393	DYS437	DYS438	DYS439	DYS448	DYS456	DYS458	DYS635	YGATAH4
1	15	14	16	23	10	11	15	14	10	12	21	15	16	21	11
2	15	14	16	22	10	13	13	14	13	12	18	15	17	20	12
3	14	11	16	23	10	14	12	15	11	12	20	15	18	21	11
4	16	12	17	24	10	13	12	14	10	12	19	15	18	23	12
5	15	14	16	22	10	13	13	14	13	12	18	15	19	20	12
6	16	14	17	25	10	11	13	14	10	12	19	15	15	21	11
7	16	14	15	23	10	13	13	14	13	12	18	15	17	21	11
8	15	13	17	24	10	11	13	14	11	12	16	15	16	21	11
9	15	14	16	22	10	13	13	14	13	12	18	15	18	20	12
10	15	14	15	22	10	13	13	14	13	12	18	15	19	20	12
11	15	12	16	23	10	12	12	15	10	12	19	15	18	20	12
12	17	14	17	25	10	11	13	14	10	12	19	15	15	21	11
13	15	13	17	25	10	11	13	14	10	12	17	16	15	21	12
14	15	13	17	24	10	13	11	15	10	12	20	15	16	20	11
15	13	13	16	24	10	11	14	14	10	13	18	16	19	21	12
16	16	11	16	23	11	12	12	15	10	13	19	16	18	20	11
17	14	12	16	24	10	14	12	15	11	12	20	15	18	20	12
18	14	13	16	23	10	14	13	14	10	11	19	15	16	22	12
19	15	12	16	23	10	14	13	14	10	12	18	16	16	21	11
20	16	12	16	25	10	13	12	14	10	12	19	14	18	22	12
21	15	13	17	25	10	13	14	14	10	12	18	14	18	22	10
22	17	13	17	25	10	11	13	14	10	12	18	15	16	22	12
23	16	12	17	24	10	13	12	15	10	11	20	15	16	21	12
24	15	14	18	23	10	12	12	14	11	12	18	15	17	21	11
25	16	13	16	23	10	11	14	14	9	12	18	15	16	21	12

^* Please note that DYS389I was substracted from DYS389II

Population studies

Watahiki H., Fujii K., Fukagawa T., Mita Y., Kitayama T. and Mizuno N. (2019), 'Polymorphisms and microvariant sequences in the Japanese population for 25 Y-STR markers and their relationships to Y-chromosome haplogroups', For Sci Int Genet 41:e1-e7 [DOI]
Kwak KD., Jin HJ., Shin DJ., Kim JM., Roewer L., Krawczak M., Tyler-Smith C. and Kim W. (2005), 'Y-chromosomal STR haplotypes and their applications to forensic and population studies in east Asia.', Int J Legal Med 119(4):195-201 [PubMed] [DOI]
Uchihi R., Yamamoto T., Usuda K., Yoshimoto T., Tanaka M., Tokunaga S., Kurihara R., Tokunaga K. and Katsumata Y. (2003), 'Haplotype analysis with 14 Y-STR loci using 2 multiplex amplification and typing systems in 2 regional populations in Japan.', Int J Legal Med 117(1):34-8 [PubMed] [DOI]
Lessig R., Willuweit S., Krawczak M., Wu FC., Pu CE., Kim W., Henke L., Henke J., Miranda J., Hidding M., Benecke M., Schmitt C., Magno M., Calacal G., Delfin FC., Ungria D., Elias S., Augustin C., Tun Z., Honda K., Kayser M., Gusmao L., Amorim A., Alves C., Hou Y., Keyser C., Ludes B., Klintschar M., Immel UD., Reichenpfader B., Zaharova B. and Roewer L. (2003), 'Asian online Y-STR Haplotype Reference Database.', Leg Med (Tokyo) 5 Suppl 1:S160-3 [PubMed]
Mizuno N., Nakahara H., Sekiguchi K., Yoshida K., Nakano M. and Kasai K. (2008), '16 Y chromosomal STR haplotypes in Japanese.', Forensic Sci Int 174(1):71-6 [PubMed] [DOI]
Purps J., Siegert S., Willuweit S., Nagy M., Alves C., Salazar R., Angustia SM., Santos LH., Anslinger K., Bayer B., Ayub Q., Wei W., Xue Y., Tyler-Smith C., Bafalluy MB., Martínez-Jarreta B., Egyed B., Balitzki B., Tschumi S., Ballard D., Court DS., Barrantes X., Bäßler G., Wiest T., Berger B., Niederstätter H., Parson W., Davis C., Budowle B., Burri H., Borer U., Koller C., Carvalho EF., Domingues PM., Chamoun WT., Coble MD., Hill CR., Corach D., Caputo M., D'Amato ME., Davison S., Decorte R., Larmuseau MH., Ottoni C., Rickards O., Lu D., Jiang C., Dobosz T., Jonkisz A., Frank WE., Furac I., Gehrig C., Castella V., Grskovic B., Haas C., Wobst J., Hadzic G., Drobnic K., Honda K., Hou Y., Zhou D., Li Y., Hu S., Chen S., Immel UD., Lessig R., Jakovski Z., Ilievska T., Klann AE., García CC., Knijff D., Kraaijenbrink T., Kondili A., Miniati P., Vouropoulou M., Kovacevic L., Marjanovic D., Lindner I., Mansour I., Al-Azem M., Andari AE., Marino M., Furfuro S., Locarno L., Martín P., Luque GM., Alonso A., Miranda LS., Moreira H., Mizuno N., Iwashima Y., Neto RS., Nogueira TL., Silva R., Nastainczyk-Wulf M., Edelmann J., Kohl M., Nie S., Wang X., Cheng B., Núñez C., Pancorbo MM., Olofsson JK., Morling N., Onofri V., Tagliabracci A., Pamjav H., Volgyi A., Barany G., Pawlowski R., Maciejewska A., Pelotti S., Pepinski W., Abreu-Glowacka M., Phillips C., Cárdenas J., Rey-Gonzalez D., Salas A., Brisighelli F., Capelli C., Toscanini U., Piccinini A., Piglionica M., Baldassarra SL., Ploski R., Konarzewska M., Jastrzebska E., Robino C., Sajantila A., Palo JU., Guevara E., Salvador J., Ungria MC., Rodriguez JJ., Schmidt U., Schlauderer N., Saukko P., Schneider PM., Sirker M., Shin KJ., Oh YN., Skitsa I., Ampati A., Smith TG., Calvit LS., Stenzl V., Capal T., Tillmar A., Nilsson H., Turrina S., Leo D., Verzeletti A., Cortellini V., Wetton JH., Gwynne GM., Jobling MA., Whittle MR., Sumita DR., Wolańska-Nowak P., Yong RY., Krawczak M., Nothnagel M. and Roewer L. (2014), 'A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.', Forensic Sci Int Genet 12:12-23 [PubMed] [DOI]
Xu H., Wang CC., Shrestha R., Wang LX., Zhang M., He Y., Kidd JR., Kidd KK., Jin L. and Li H. (2015), 'Inferring population structure and demographic history using Y‐STR data from worldwide populations', Mol Genet Genomics 290(1):141-50 [DOI]

Personal communication

YA005597

	DYS19	DYS389I	DYS389II^*	DYS390	DYS391	DYS392	DYS393
1	16	13	16	23	10	11	14
2	15	14	16	22	10	13	13
3	14	12	16	24	10	14	12
4	16	12	17	24	10	13	12
5	16	14	17	25	10	11	13
6	16	14	15	23	10	13	13
7	15	13	16	24	10	13	12
8	15	12	16	23	10	12	12
9	15	14	17	25	10	11	13
10	17	13	17	25	10	11	13
11	15	14	16	23	10	11	15
12	15	14	15	22	10	13	13
13	17	14	17	25	10	11	13
14	15	13	17	25	10	11	13
15	13	13	16	24	10	11	14
16	14	13	16	23	10	14	13
17	15	13	16	22	10	13	13
18	17	12	16	25	10	13	12
19	16	11	16	23	11	12	12
20	15	12	17	24	10	14	14
21	15	13	15	22	10	13	13
22	15	14	18	23	10	12	12

	DYS19	DYS389I	DYS389II^*	DYS390	DYS391	DYS392	DYS393	DYS437	DYS438	DYS439	DYS448	DYS456	DYS458	DYS635	YGATAH4
1	15	14	16	23	10	11	15	14	10	12	21	15	16	21	11
2	15	14	16	22	10	13	13	14	13	12	18	15	17	20	12
3	14	11	16	23	10	14	12	15	11	12	20	15	18	21	11
4	16	12	17	24	10	13	12	14	10	12	19	15	18	23	12
5	15	14	16	22	10	13	13	14	13	12	18	15	19	20	12
6	16	14	17	25	10	11	13	14	10	12	19	15	15	21	11
7	16	14	15	23	10	13	13	14	13	12	18	15	17	21	11
8	15	13	17	24	10	11	13	14	11	12	16	15	16	21	11
9	15	14	16	22	10	13	13	14	13	12	18	15	18	20	12
10	15	14	15	22	10	13	13	14	13	12	18	15	19	20	12
11	15	12	16	23	10	12	12	15	10	12	19	15	18	20	12
12	17	14	17	25	10	11	13	14	10	12	19	15	15	21	11
13	15	13	17	25	10	11	13	14	10	12	17	16	15	21	12
14	15	13	17	24	10	13	11	15	10	12	20	15	16	20	11
15	13	13	16	24	10	11	14	14	10	13	18	16	19	21	12
16	16	11	16	23	11	12	12	15	10	13	19	16	18	20	11
17	14	12	16	24	10	14	12	15	11	12	20	15	18	20	12
18	14	13	16	23	10	14	13	14	10	11	19	15	16	22	12
19	15	12	16	23	10	14	13	14	10	12	18	16	16	21	11
20	16	12	16	25	10	13	12	14	10	12	19	14	18	22	12
21	15	13	17	25	10	13	14	14	10	12	18	14	18	22	10
22	17	13	17	25	10	11	13	14	10	12	18	15	16	22	12
23	16	12	17	24	10	13	12	15	10	11	20	15	16	21	12
24	15	14	18	23	10	12	12	14	11	12	18	15	17	21	11
25	16	13	16	23	10	11	14	14	9	12	18	15	16	21	12

	DYS19	DYS389I	DYS389II^*	DYS390	DYS391	DYS392	DYS393
1	16	13	16	23	10	11	14
2	15	14	16	22	10	13	13
3	14	12	16	24	10	14	12
4	16	12	17	24	10	13	12
5	16	14	17	25	10	11	13
6	16	14	15	23	10	13	13
7	15	13	16	24	10	13	12
8	15	12	16	23	10	12	12
9	15	14	17	25	10	11	13
10	17	13	17	25	10	11	13
11	15	14	16	23	10	11	15
12	15	14	15	22	10	13	13
13	17	14	17	25	10	11	13
14	15	13	17	25	10	11	13
15	13	13	16	24	10	11	14
16	14	13	16	23	10	14	13
17	15	13	16	22	10	13	13
18	17	12	16	25	10	13	12
19	16	11	16	23	11	12	12
20	15	12	17	24	10	14	14
21	15	13	15	22	10	13	13
22	15	14	18	23	10	12	12

	DYS19	DYS389I	DYS389II^*	DYS390	DYS391	DYS392	DYS393	DYS437	DYS438	DYS439	DYS448	DYS456	DYS458	DYS635	YGATAH4
1	15	14	16	23	10	11	15	14	10	12	21	15	16	21	11
2	15	14	16	22	10	13	13	14	13	12	18	15	17	20	12
3	14	11	16	23	10	14	12	15	11	12	20	15	18	21	11
4	16	12	17	24	10	13	12	14	10	12	19	15	18	23	12
5	15	14	16	22	10	13	13	14	13	12	18	15	19	20	12
6	16	14	17	25	10	11	13	14	10	12	19	15	15	21	11
7	16	14	15	23	10	13	13	14	13	12	18	15	17	21	11
8	15	13	17	24	10	11	13	14	11	12	16	15	16	21	11
9	15	14	16	22	10	13	13	14	13	12	18	15	18	20	12
10	15	14	15	22	10	13	13	14	13	12	18	15	19	20	12
11	15	12	16	23	10	12	12	15	10	12	19	15	18	20	12
12	17	14	17	25	10	11	13	14	10	12	19	15	15	21	11
13	15	13	17	25	10	11	13	14	10	12	17	16	15	21	12
14	15	13	17	24	10	13	11	15	10	12	20	15	16	20	11
15	13	13	16	24	10	11	14	14	10	13	18	16	19	21	12
16	16	11	16	23	11	12	12	15	10	13	19	16	18	20	11
17	14	12	16	24	10	14	12	15	11	12	20	15	18	20	12
18	14	13	16	23	10	14	13	14	10	11	19	15	16	22	12
19	15	12	16	23	10	14	13	14	10	12	18	16	16	21	11
20	16	12	16	25	10	13	12	14	10	12	19	14	18	22	12
21	15	13	17	25	10	13	14	14	10	12	18	14	18	22	10
22	17	13	17	25	10	11	13	14	10	12	18	15	16	22	12
23	16	12	17	24	10	13	12	15	10	11	20	15	16	21	12
24	15	14	18	23	10	12	12	14	11	12	18	15	17	21	11
25	16	13	16	23	10	11	14	14	9	12	18	15	16	21	12