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Wild Oryza 217 Genome Sequence Data

This shows the sequence data of 217 accessions from 19 wild Oryza species. Each accession has sequence information of illumination short reads (100-150 bp) of over 10x depth and is linked by the DRR registration number shown in the Table. Phylogenetic relations of wild Oryza can be viewed from here.

Phylogenetic tree
Oryzagenome2 Phylogenetic tree

Phylogenetic relationship of Oryza genus drawn by NJ method using polymorphisms against O. sativa, Nipponbare chloroplast DNA. Leersia perrieri is used as an outgroup. Redrawn from Shenton et al., (2020) Genome Biology and Evolution 12 (4), 413-428.

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IDAcc. No.DRR No.Acc. details and material requestNIG Core collection rank
SpeciesGenome
Origin / CountryRemarks
217IRGC105908
DRR226074 (NCBI, DDBJ)
IRGC105908, VCF
no RankO. rufipogonAA
216IRGC105715
DRR226073 (NCBI, DDBJ)
IRGC105715, VCF
no RankO. rufipogonAA
215IRGC105668
DRR057991 (NCBI, DDBJ)
IRGC105668
no RankO. glumaepatulaAA
214IRGC105444
DRR226072 (NCBI, DDBJ)
IRGC105444, VCF
no RankO. rufipogonAA
213W2263
DRR226071 (NCBI, DDBJ)
W2263, VCF
Rank2O. rufipogonAACambodiaOr-I
212W2220
DRR056802 (NCBI, DDBJ)
W2220
Rank1O. grandiglumisCCDDBrazil
211W2203
DRR058011 (NCBI, DDBJ)
W2203
Rank3O. glumaepatulaAABrazil
210W2201
DRR058010 (NCBI, DDBJ)
W2201
Rank3O. glumaepatulaAABrazil
209W2200
DRR056795 (NCBI, DDBJ)
W2200
Rank1O. latifoliaCCDDBrazil
208W2199
DRR058009 (NCBI, DDBJ)
W2199
Rank1O. glumaepatulaAABrazil
207W2192
DRR058008 (NCBI, DDBJ)
W2192
Rank3O. glumaepatulaAABrazil
206W2184
DRR058007 (NCBI, DDBJ)
W2184
Rank3O. glumaepatulaAABrazil
205W2173
DRR058006 (NCBI, DDBJ)
W2173
Rank3O. glumaepatulaAABrazil
204W2165
DRR058005 (NCBI, DDBJ)
W2165
Rank3O. glumaepatulaAABrazil
203W2160
DRR058004 (NCBI, DDBJ)
W2160
Rank3O. glumaepatulaAABrazil
202W2149
DRR058003 (NCBI, DDBJ)
W2149
Rank3O. glumaepatulaAABrazil
201W2145
DRR058002 (NCBI, DDBJ)
W2145
Rank1O. glumaepatulaAABrazil
200W2140
DRR058001 (NCBI, DDBJ)
W2140
Rank3O. glumaepatulaAABrazil
199W2117
DRR058030 (NCBI, DDBJ)
W2117, VCF
no RankO. rufipogon/O. meridionalisAAAustralia
198W2116
DRR058029 (NCBI, DDBJ)
W2116
Rank3O. meridionalisAAAustralia
197W2114
DRR058028 (NCBI, DDBJ)
W2114, VCF
no RankO. rufipogon/O. meridionalisAAAustralia
196W2112
DRR058027 (NCBI, DDBJ)
W2112
Rank3O. meridionalisAAAustralia
195W2109
DRR226070 (NCBI, DDBJ)
W2109, VCF
Rank3O. rufipogonAAAustralia
194W2105
DRR058026 (NCBI, DDBJ)
W2105
Rank3O. meridionalisAAAustralia
193W2104
DRR056785 (NCBI, DDBJ)
W2104
Rank2O. australiensisEEAustralia
192W2103
DRR058025 (NCBI, DDBJ)
W2103
Rank2O. meridionalisAAAustralia
191W2100
DRR226069 (NCBI, DDBJ)
W2100
Rank3O. meridionalisAAAustralia
190W2086
DRR056784 (NCBI, DDBJ)
W2086
Rank2O. australiensisEEAustralia
189W2084
DRR056783 (NCBI, DDBJ)
W2084
Rank3O. australiensisEEAustralia
188W2082
DRR056782 (NCBI, DDBJ)
W2082
Rank3O. australiensisEEAustralia
187W2081
DRR058024 (NCBI, DDBJ)
W2081
Rank3O. meridionalisAAAustralia
186W2080
DRR058023 (NCBI, DDBJ)
W2080
Rank3O. meridionalisAAAustralia
185W2079
DRR058022 (NCBI, DDBJ)
W2079
Rank2O. meridionalisAAAustralia
184W2078
DRR226068 (NCBI, DDBJ)
W2078, VCF
Rank2O. rufipogonAAAustraliaOr-III
183W2077
DRR226067 (NCBI, DDBJ)
W2077
Rank3O. meridionalisAAAustralia
182W2072
DRR056781 (NCBI, DDBJ)
W2072
Rank3O. australiensisEEAustralia
181W2071
DRR058021 (NCBI, DDBJ)
W2071
Rank3O. meridionalisAAAustralia
180W2069
DRR058020 (NCBI, DDBJ)
W2069
Rank2O. meridionalisAAAustralia
179W2068
DRR056674 (NCBI, DDBJ)
W2068
Rank2O. meyerianaGG
178W2057
SRR1016487 (NCBI, DDBJ)
SRR1016488 (NCBI, DDBJ)
W2057, VCF
no RankO. rufipogonAABangladeshOr-III
177W2051
DRR226066 (NCBI, DDBJ)
W2051, VCF
Rank2O. rufipogonAABangladeshOr-II
176W2035
DRR056665 (NCBI, DDBJ)
W2035
Rank2O. ridleyiHHJJThailand
175W2003
DRR226065 (NCBI, DDBJ)
SRR1016485 (NCBI, DDBJ)
SRR1016486 (NCBI, DDBJ)
W2003, VCF
Rank1O. rufipogonAAIndiaOr-III
174W1981
DRR001190 (NCBI, DDBJ)
W1981, VCF
Rank3O. rufipogonAAIndonesiaOr-II
173W1976
SRR1016481 (NCBI, DDBJ)
SRR1016482 (NCBI, DDBJ)
W1976, VCF
no RankO. rufipogonAAIndonesiaOr-II
172W1965
SRR1016475 (NCBI, DDBJ)
SRR1016476 (NCBI, DDBJ)
W1965, VCF
no RankO. rufipogonAAChina
171W1962
DRR226064 (NCBI, DDBJ)
W1962, VCF
no RankO. rufipogonAAChina
170W1945
DRR226063 (NCBI, DDBJ)
W1945, VCF
Rank2O. rufipogonAAOr-III
169W1930
DRR057222 (NCBI, DDBJ)
W1930
Rank3O. officinalisCCThailand
168W1921
DRR226062 (NCBI, DDBJ)
DRR000347 (NCBI, DDBJ)
DRR000465 (NCBI, DDBJ)
W1921, VCF
Rank1O. rufipogonAAThailandOr-I
167W1886
SRR1016492 (NCBI, DDBJ)
SRR1016493 (NCBI, DDBJ)
W1886, VCF
no RankO. rufipogonAAThailand
166W1866
DRR226061 (NCBI, DDBJ)
W1866, VCF
Rank1O. rufipogonAAThailandOr-I
165W1830
DRR057221 (NCBI, DDBJ)
W1830
Rank1O. officinalisCC
164W1814
DRR057220 (NCBI, DDBJ)
W1814
Rank2O. officinalisCCSri Lanka
163W1808
DRR054692 (NCBI, DDBJ)
W1808
Rank3O. rhizomatisCCSri Lanka
162W1807
DRR226060 (NCBI, DDBJ)
SRR1016483 (NCBI, DDBJ)
SRR1016484 (NCBI, DDBJ)
W1807, VCF
Rank2O. rufipogonAASri LankaOr-III
161W1805
DRR055281 (NCBI, DDBJ)
W1805
Rank1O. rhizomatisCCSri Lanka
160W1715
DRR226059 (NCBI, DDBJ)
DRR001187 (NCBI, DDBJ)
W1715, VCF
Rank3O. rufipogonAAChinaOr-II
159W1712
DRR053309 (NCBI, DDBJ)
W1712
Rank3O. brachyanthaFFCameroun
158W1711
DRR053308 (NCBI, DDBJ)
W1711
Rank1O. brachyanthaFFCameroun
157W1708
DRR053307 (NCBI, DDBJ)
W1708
Rank3O. brachyanthaFFCameroun
156W1706
DRR053306 (NCBI, DDBJ)
W1706
Rank2O. brachyanthaFFTchad (=Chad)
155W1705
DRR053305 (NCBI, DDBJ)
W1705
Rank3O. brachyanthaFFMali
154W1703
DRR053304 (NCBI, DDBJ)
W1703
Rank3O. brachyanthaFFMali
153W1702
DRR057990 (NCBI, DDBJ)
W1702
Rank3O. barthiiAAMali
152W1681
DRR226058 (NCBI, DDBJ)
W1681, VCF
Rank3O. rufipogonAAIndiaOr-I
151W1669
DRR226057 (NCBI, DDBJ)
W1669, VCF
Rank3O. rufipogonAAIndiaOr-III
150W1650
DRR058048 (NCBI, DDBJ)
W1650
Rank3O. longistaminataAATanzania
149W1646
DRR057989 (NCBI, DDBJ)
W1646
Rank2O. barthiiAATanzania
148W1643
DRR057988 (NCBI, DDBJ)
W1643
Rank3O. barthiiAABotswana
147W1642
DRR057987 (NCBI, DDBJ)
W1642
Rank3O. barthiiAABotswana
146W1638
DRR058019 (NCBI, DDBJ)
W1638
Rank3O. meridionalisAAAustralia
145W1635
DRR058018 (NCBI, DDBJ)
W1635
Rank1O. meridionalisAAAustralia
144W1632
DRR056780 (NCBI, DDBJ)
W1632
Rank2O. australiensisEEAustralia
143W1631
DRR058017 (NCBI, DDBJ)
W1631
Rank3O. meridionalisAAAustralia
142W1628
DRR056779 (NCBI, DDBJ)
W1628
Rank1O. australiensisEEAustralia
141W1627
DRR058016 (NCBI, DDBJ)
W1627
Rank2O. meridionalisAAAustralia
140W1625
DRR058014 (NCBI, DDBJ)
W1625
Rank1O. meridionalisAAAustralia
139W1624
DRR058047 (NCBI, DDBJ)
W1624
Rank2O. longistaminataAACameroun
138W1605
DRR057986 (NCBI, DDBJ)
W1605
Rank3O. barthiiAANigeria
137W1593
DRR056222 (NCBI, DDBJ)
W1593
Rank3O. punctata (2X)BBNigeria
136W1592
DRR056221 (NCBI, DDBJ)
W1592
Rank3O. punctata (2X)BBCameroun
135W1590
DRR056219 (NCBI, DDBJ)
W1590
Rank2O. punctata (2X)BBCameroun
134W1588
DRR057985 (NCBI, DDBJ)
W1588
Rank1O. barthiiAACameroun
133W1586
DRR056218 (NCBI, DDBJ)
W1586
Rank3O. punctata (2X)BBTchad (=Chad)
132W1583
DRR057984 (NCBI, DDBJ)
W1583
Rank3O. barthiiAATchad (=Chad)
131W1582
DRR056217 (NCBI, DDBJ)
W1582
Rank3O. punctata (2X)BBTchad (=Chad)
130W1577
DRR056216 (NCBI, DDBJ)
W1577
Rank3O. punctata (2X)BBNigeria
129W1574
DRR057983 (NCBI, DDBJ)
W1574
Rank3O. barthiiAANigeria
128W1573
DRR058046 (NCBI, DDBJ)
W1573
Rank3O. longistaminataAANigeria
127W1564
DRR057969 (NCBI, DDBJ)
W1564
Rank3O. punctata (4X)BBCCNigeria
126W1551
DRR226056 (NCBI, DDBJ)
W1551, VCF
Rank3O. rufipogonAAThailandOr-I
125W1540
DRR058045 (NCBI, DDBJ)
W1540
Rank2O. longistaminataAACongo
124W1539
DRR056794 (NCBI, DDBJ)
W1539
Rank3O. latifoliaCCDDArgentina
123W1527
DRR057208 (NCBI, DDBJ)
W1527
Rank1O. eichingeriCCUganda
122W1526
DRR057207 (NCBI, DDBJ)
W1526
Rank3O. eichingeriCCUganda
121W1522
DRR057206 (NCBI, DDBJ)
W1522
Rank2O. eichingeriCCUganda
120W1519
DRR057205 (NCBI, DDBJ)
W1519
Rank2O. eichingeriCCUganda
119W1515
DRR056215 (NCBI, DDBJ)
W1515
Rank3O. punctata (2X)BBTanganyika
118W1514
DRR056213 (NCBI, DDBJ)
W1514
Rank1O. punctata (2X)BBKenya
117W1508
DRR058044 (NCBI, DDBJ)
W1508
Rank1O. longistaminataAAMadagascar
116W1504
DRR058043 (NCBI, DDBJ)
W1504
Rank3O. longistaminataAATanganyika
115W1483
DRR056801 (NCBI, DDBJ)
W1483
Rank3O. grandiglumisCCDDBrazil
114W1480(B)
DRR056800 (NCBI, DDBJ)
W1480(B)
Rank2O. grandiglumisCCDDBrazil
113W1477
DRR058000 (NCBI, DDBJ)
W1477
Rank3O. glumaepatulaAABrazil
112W1476
DRR056799 (NCBI, DDBJ)
W1476
Rank2O. grandiglumisCCDDBrazil
111W1473
DRR057982 (NCBI, DDBJ)
W1473
Rank3O. barthiiAATchad (=Chad)
110W1467
DRR057981 (NCBI, DDBJ)
W1467
Rank3O. barthiiAACameroun
109W1465
DRR058042 (NCBI, DDBJ)
W1465
Rank3O. longistaminataAANigeria
108W1460
DRR058041 (NCBI, DDBJ)
W1460
Rank3O. longistaminataAADahomey
107W1454(B)
DRR058040 (NCBI, DDBJ)
W1454(B)
Rank3O. longistaminataAAUpper Volta (Burkina Faso)
106W1448
DRR058039 (NCBI, DDBJ)
W1448
Rank3O. longistaminataAAIvory Coast
105W1444
DRR058038 (NCBI, DDBJ)
W1444
Rank3O. longistaminataAAIvory Coast
104W1443(A)
DRR057980 (NCBI, DDBJ)
W1443(A)
Rank3O. barthiiAAMali
103W1423
DRR058037 (NCBI, DDBJ)
W1423
Rank3O. longistaminataAAMali
102W1420
DRR058036 (NCBI, DDBJ)
W1420
Rank3O. longistaminataAAMali
101W1416
DRR057979 (NCBI, DDBJ)
W1416
Rank3O. barthiiAASierra LeoneLocal name : Yerr-yerr
100W1413
DRR058035 (NCBI, DDBJ)
W1413
Rank1O. longistaminataAASierra Leone
99W1410
DRR057978 (NCBI, DDBJ)
W1410
Rank3O. barthiiAASierra Leone
98W1409
DRR057968 (NCBI, DDBJ)
W1409
Rank3O. punctata (4X)BBCCNigeria
97W1408
DRR057967 (NCBI, DDBJ)
W1408
Rank2O. punctata (4X)BBCCNigeria
96W1407(B)
DRR053303 (NCBI, DDBJ)
W1407(B)
Rank2O. brachyanthaFFMali
95W1405
DRR053302 (NCBI, DDBJ)
W1405
Rank3O. brachyanthaFFSierra Leone
94W1404
DRR053301 (NCBI, DDBJ)
W1404
Rank3O. brachyanthaFFSierra Leone
93W1403
DRR053300 (NCBI, DDBJ)
W1403
Rank3O. brachyanthaFFSierra Leone
92W1402
DRR053299 (NCBI, DDBJ)
W1402
Rank3O. brachyanthaFFSierra Leone
91W1401
DRR053298 (NCBI, DDBJ)
W1401
Rank1O. brachyanthaFFSierra Leone
90W1361
DRR057219 (NCBI, DDBJ)
W1361
Rank1O. officinalisCCMalaysia
89W1360
DRR056673 (NCBI, DDBJ)
W1360
Rank2O. meyerianaGGMalaysia
88W1356
DRR056672 (NCBI, DDBJ)
W1356
Rank1O. meyerianaGGMalaysia
87W1352
DRR056671 (NCBI, DDBJ)
W1352
Rank2O. meyerianaGGMalaysia
86W1348
DRR056670 (NCBI, DDBJ)
W1348
Rank2O. meyerianaGGMalaysia
85W1344
DRR057961 (NCBI, DDBJ)
W1344
Rank3O. minutaBBCCPhilippines
84W1342
DRR057960 (NCBI, DDBJ)
W1342
Rank3O. minutaBBCCPhilippines
83W1331
DRR057959 (NCBI, DDBJ)
W1331
Rank1O. minutaBBCCPhilippines
82W1329
DRR057958 (NCBI, DDBJ)
W1329
Rank2O. minutaBBCCPhilippines
81W1328
DRR057957 (NCBI, DDBJ)
W1328
Rank2O. minutaBBCCPhilippines
80W1323
DRR057954 (NCBI, DDBJ)
W1323
Rank2O. minutaBBCCPhilippines
79W1319
DRR057953 (NCBI, DDBJ)
W1319
Rank2O. minutaBBCCPhilippines
78W1315
DRR057218 (NCBI, DDBJ)
W1315
Rank3O. officinalisCCPhilippines
77W1308
DRR057217 (NCBI, DDBJ)
W1308
Rank3O. officinalisCCPhilippines
76W1302
DRR057216 (NCBI, DDBJ)
W1302
Rank2O. officinalisCCPhilippines
75W1301
DRR057215 (NCBI, DDBJ)
W1301
Rank3O. officinalisCCMalaysia
74W1300
DRR058013 (NCBI, DDBJ)
W1300
Rank3O. meridionalisAAAustralia
73W1297
DRR058012 (NCBI, DDBJ)
W1297
Rank2O. meridionalisAAAustralia
72W1294
SRR1016480 (NCBI, DDBJ)
W1294, VCF
Rank1O. rufipogonAAPhilippinesOr-III
71W1291
DRR057214 (NCBI, DDBJ)
W1291
Rank3O. officinalisCCIndonesiaLocal name : Padi Kujang
70W1270
DRR057213 (NCBI, DDBJ)
W1270
Rank3O. officinalisCCBrunei
69W1252
DRR057212 (NCBI, DDBJ)
W1252
Rank3O. officinalisCCMalaysia
68W1247
DRR056798 (NCBI, DDBJ)
W1247
Rank3O. grandiglumisCCDDBrazil
67W1236
DRR001184 (NCBI, DDBJ)
W1236, VCF
Rank2O. rufipogonAAAustralian New Guinea (Papua New Guinea)Or-II
66W1232
DRR058034 (NCBI, DDBJ)
W1232
Rank3O. longistaminataAATanganyika
65W1230
DRR001189 (NCBI, DDBJ)
W1230, VCF
Rank3O. rufipogonAADutch New Guinea (Indonesia)Or-I
64W1229
DRR056662 (NCBI, DDBJ)
W1229
Rank1O. longiglumisHHJJDutch New Guinea (Indonesia)
63W1228
DRR056661 (NCBI, DDBJ)
W1228
Rank2O. longiglumisHHJJDutch New Guinea (Indonesia)
62W1224
DRR056660 (NCBI, DDBJ)
W1224
Rank2O. longiglumisHHJJDutch New Guinea (Indonesia)
61W1220
DRR056659 (NCBI, DDBJ)
W1220
Rank1O. longiglumisHHJJDutch New Guinea (Indonesia)
60W1215
DRR056658 (NCBI, DDBJ)
W1215
Rank2O. longiglumisHHJJDutch New Guinea (Indonesia)
59W1213
DRR057956 (NCBI, DDBJ)
W1213
Rank1O. minutaBBCCPhilippines
58W1200
DRR057211 (NCBI, DDBJ)
W1200
Rank3O. officinalisCCPhilippines
57W1197
DRR056793 (NCBI, DDBJ)
W1197
Rank1O. latifoliaCCDDColombia
56W1196
DRR057999 (NCBI, DDBJ)
W1196
Rank2O. glumaepatulaAAColombia
55W1194
DRR056797 (NCBI, DDBJ)
W1194
Rank1O. grandiglumisCCDDBrazil
54W1191
DRR057998 (NCBI, DDBJ)
W1191
Rank3O. glumaepatulaAABrazil
53W1189
DRR057997 (NCBI, DDBJ)
W1189
Rank3O. glumaepatulaAABrazil
52W1187
DRR057996 (NCBI, DDBJ)
W1187
Rank2O. glumaepatulaAABrazil
51W1185
DRR057995 (NCBI, DDBJ)
W1185
Rank2O. glumaepatulaAASuriname
50W1184
DRR056792 (NCBI, DDBJ)
W1184
Rank3O. latifoliaCCDDSuriname
49W1183
DRR057994 (NCBI, DDBJ)
W1183
Rank3O. glumaepatulaAABritish Guiana
48W1182
DRR056788 (NCBI, DDBJ)
W1182
Rank1O. alta/ O. latifoliaCCDDBritish Guiana
47W1181
DRR056791 (NCBI, DDBJ)
W1181
Rank2O. latifoliaCCDDPanama
46W1171
DRR057993 (NCBI, DDBJ)
W1171
Rank3O. glumaepatulaAACuba
45W1169=W1165
DRR057992 (NCBI, DDBJ)
W1169=W1165
Rank1O. glumaepatulaAACuba
44W1166
DRR056790 (NCBI, DDBJ)
W1166
Rank1O. latifoliaCCDDMexico
43W1147
DRR056787 (NCBI, DDBJ)
W1147
Rank2O. altaCCDDSurinam (?)
42W1145
DRR057966 (NCBI, DDBJ)
W1145
Rank3O. punctata (4X)BBCCBelgium Congo (Congo)
41W1063
DRR057977 (NCBI, DDBJ)
W1063
Rank3O. barthiiAA
40W1057
DRR053297 (NCBI, DDBJ)
W1057
Rank3O. brachyanthaFFGuinea
39W1050
DRR057976 (NCBI, DDBJ)
W1050
Rank3O. barthiiAAGambia
38W1024
DRR057965 (NCBI, DDBJ)
W1024
Rank1O. punctata (4X)BBCCGhana
37W1023
DRR057964 (NCBI, DDBJ)
W1023
Rank3O. punctata (4X)BBCCGhana
36W1004
DRR058033 (NCBI, DDBJ)
W1004
Rank3O. longistaminataAAGhana
35W0747
DRR057975 (NCBI, DDBJ)
W0747
Rank2O. barthiiAAMali
34W0720
DRR057974 (NCBI, DDBJ)
W0720
Rank2O. barthiiAAMali
33W0708
DRR058032 (NCBI, DDBJ)
W0708
Rank2O. longistaminataAAGuinea
32W0698
DRR057973 (NCBI, DDBJ)
W0698
Rank2O. barthiiAAGuinea
31W0656
DRR053296 (NCBI, DDBJ)
W0656
Rank2O. brachyanthaFFGuinea
30W0655
DRR053295 (NCBI, DDBJ)
W0655
Rank3O. brachyanthaFFSierra Leone
29W0654
DRR053294 (NCBI, DDBJ)
W0654
Rank3O. brachyanthaFFSierra Leone
28W0652
DRR057972 (NCBI, DDBJ)
W0652
Rank1O. barthiiAASierra Leone
27W0643
DRR058031 (NCBI, DDBJ)
W0643
Rank2O. longistaminataAAGambia
26W0630
DRR226055 (NCBI, DDBJ)
SRR1016489 (NCBI, DDBJ)
SRR1016490 (NCBI, DDBJ)
SRR1016491 (NCBI, DDBJ)
DRR001185 (NCBI, DDBJ)
W0630, VCF
Rank2O. rufipogonAABurmaOr-I
25W0615
DRR056669 (NCBI, DDBJ)
W0615
Rank2O. granulataGGBurma
24W0613
DRR056796 (NCBI, DDBJ)
W0613
Rank1O. grandiglumisCCDDBrazil
23W0604
DRR056664 (NCBI, DDBJ)
W0604
Rank1O. ridleyiHHJJMalaya (Malaysia)
22W0593
SRR1016473 (NCBI, DDBJ)
SRR1016474 (NCBI, DDBJ)
DRR001183 (NCBI, DDBJ)
W0593, VCF
Rank3O. rufipogonAAMalaya (Malaysia) Or-III
21W0566
DRR057210 (NCBI, DDBJ)
W0566
Rank3O. officinalisCCMalaya (Malaysia)
20W0542
DRR056789 (NCBI, DDBJ)
W0542
Rank3O. latifoliaCCDDMexico
19W0180
DRR001188 (NCBI, DDBJ)
W0180, VCF
Rank3O. rufipogonAAThailandOr-II
18W0137
DRR226054 (NCBI, DDBJ)
W0137, VCF
Rank3O. rufipogonAAIndiaOr-III
17W0120
SRR1016477 (NCBI, DDBJ)
SRR1016478 (NCBI, DDBJ)
DRR001186 (NCBI, DDBJ)
W0120, VCF
Rank1O. rufipogonAAIndiaOr-II
16W0106
DRR000348 (NCBI, DDBJ)
DRR000466 (NCBI, DDBJ)
W0106, VCF
Rank1O. rufipogonAAIndiaOr-I
15W0067(B)
DRR056668 (NCBI, DDBJ)
W0067(B)
Rank1O. granulataGGThailand
14W0065
DRR057209 (NCBI, DDBJ)
W0065
Rank3O. officinalisCCThailand
13W0051
DRR057952 (NCBI, DDBJ)
W0051
Rank3O. minutaBBCC
12W0049
DRR057971 (NCBI, DDBJ)
W0049
no RankO. barthiiAA
11W0045
DRR057955 (NCBI, DDBJ)
W0045
Rank3O. minutaBBCC
10W0043
DRR057963 (NCBI, DDBJ)
W0043
Rank3O. punctata (4X)BBCC
9W0042
DRR057970 (NCBI, DDBJ)
W0042
Rank3O. barthiiAA
8W0017
DRR056786 (NCBI, DDBJ)
W0017
Rank1O. altaCCDDSurinam
7W0016
DRR057951 (NCBI, DDBJ)
W0016
Rank2O. minutaBBCCUnknown
6W0015
DRR057962 (NCBI, DDBJ)
W0015
Rank3O. punctata (4X) ?BBCC
5W0008
DRR056778 (NCBI, DDBJ)
W0008
Rank1O. australiensisEEAustralia(?)
4W0005
DRR056667 (NCBI, DDBJ)
W0005
Rank2O. granulataGGCeylon
3W0003
DRR056666 (NCBI, DDBJ)
W0003
Rank1O. granulataGGIndia
2W0002
DRR014203 (NCBI, DDBJ)
W0002
Rank1O. officinalisCCThailand
1W0001
DRR056663 (NCBI, DDBJ)
W0001
Rank1O. ridleyiHHJJThailand

Misc Downloads

Genotype files


  • 446 O.rufipogon accessions Tabular formatted genotype
    (space delimited, 0 = ref allele 2 = alt allele (not necessarily minor), imputed data )
  • 446 O.rufipogon accessions VCF file ( raw data , imputed data )
  • 446 O.rufipogon accessions Plink formatted genotype ( ped , map )

BED format annotations for 446 O. rufipogon SNP viewer
(Huang et a., 2012)

Fst in 446 O. rufipogon population


  • Fst values among three ecotypes in 446 O. rufipogon accessions defined by Huang et al. 2012. ( Map.Fst.txt )

Release 1.0 contents

Accession Lists

In the accession list, the first page provides information on the 446 O. rufipogon accessions including accession number, habitat/country of origin, ecotype, sequence coverage and deposited ID of NGS raw data. The second page provides information on eleven O. rufipogon, four O. sativa and two O. longistaminata accessions in the same categories. NGS raw data files for each genome can be retrieved through the public Databases DDBJ or EBI.

Download accession lists.

Variant Lists

The variant list contains datasets of genome-wide SNP information for each accession. Whole genome information of each accession is provided as a VCF (variant call format) file or a tab delimited file.


Download imputed SNPs of 446 O. rufipogon accessions