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
R67
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
R67
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
* See FAQ/Glossary (http://yhrd.org/pages/faq) for further explanations of abbreviated terms used here