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Wild Oryza 200 Genome Sequence Data


This shows the sequence data of 208 accessions from 19 wild and 2 cultivated Oryza species. All accession has sequence information of illumination short reads (100-150 bp) of over x10 depth and is linked by the DRA registration number shown in the Table.

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IDSequencedDRA No.Acc. No.Core collection rank
SpeciesGenome
RemarksOriginal place / Country
1W0001DRA004508W0001Rank1O. ridleyiHHJJPerennialThailand
2W0002DRA001178W0002Rank1O. officinalisCCPerennialThailand
3W0003DRA004509W0003Rank1O. granulataGGPerennialIndia
4W0005DRA004509W0005Rank2O. granulataGGPerennialCeylon
5W0008DRA004524W0008Rank1O. australiensisEEPerennialAustralia(?)
6W0015DRA004587W0015Rank3O. punctata (4X) ?BBCCPerennial
7W0016DRA004585W0016Rank2O. minutaBBCCPerennialUnknown
8W0017DRA004525W0017Rank1O. altaCCDDPerennialSurinam
9W0018DRA004525W0018Rank2O. altaCCDDPerennialParaguay
10W0042DRA004588W0042Rank3O. barthiiAAAnnual
11W0043DRA004587W0043Rank3O. punctata (4X)BBCCPerennial
12W0045DRA004586W0045Rank3O. minutaBBCCPerennial
13W0049DRA004588W0049Rank4O. barthiiAAAnnual
14W0051DRA004585W0051Rank3O. minutaBBCCPerennial
15W0065DRA004552W0065Rank3O. officinalisCCPerennialThailand
16W0067(B)DRA004509W0067(B)Rank1O. granulataGGPerennialThailand
17W0137DRA005599W0137Rank3O. rufipogonAAIndia
18W0542DRA004526W0542Rank3O. latifoliaCCDDPerennialMexico
19W0566DRA004552W0566Rank3O. officinalisCCPerennialMalaya (Malaysia)
20W0604DRA004508W0604Rank1O. ridleyiHHJJPerennialMalaya (Malaysia)
21W0613DRA004527W0613Rank1O. grandiglumisCCDDPerennialBrazil
22W0615DRA004509W0615Rank2O. granulataGGPerennialBurma
23W0630DRA005599W0630Rank2O. rufipogonAAAnnualBurma
24W0643DRA004591W0643Rank2O. longistaminataAAPerennialGambia
25W0652DRA004588W0652Rank1O. barthiiAAAnnualSierra Leone
26W0654DRA004336W0654Rank3O. brachyanthaFFSierra Leone
27W0655DRA004336W0655Rank3O. brachyanthaFFSierra Leone
28W0656DRA004336W0656Rank2O. brachyanthaFFGuinea
29W0698DRA004588W0698Rank2O. barthiiAAAnnualGuinea
30W0708DRA004591W0708Rank2O. longistaminataAAPerennialGuinea
31W0720DRA004588W0720Rank2O. barthiiAAAnnualMali
32W0747DRA004588W0747Rank2O. barthiiAAAnnualMali
33W1004DRA004591W1004Rank3O. longistaminataAAPerennialGhana
34W1023DRA004587W1023Rank3O. punctata (4X)BBCCPerennialGhana
35W1024DRA004587W1024Rank1O. punctata (4X)BBCCPerennialGhana
36W1050DRA004588W1050Rank3O. barthiiAAAnnualGambia
37W1057DRA004336W1057Rank3O. brachyanthaFFGuinea
38W1063DRA004588W1063Rank3O. barthiiAAAnnual
39W1145DRA004587W1145Rank3O. punctata (4X)BBCCPerennialBelgium Congo (Congo)
40W1147DRA004525W1147Rank2O. altaCCDDSurinam (?)
41W1166DRA004526W1166Rank1O. latifoliaCCDDPerennialMexico
42W1169=W1165DRA004589W1169=W1165Rank1O. glumaepatulaAAPerennialCuba
43W1171DRA004589W1171Rank3O. glumaepatulaAACuba
44W1181DRA004526W1181Rank2O. latifoliaCCDDPerennialPanama
45W1183DRA004589W1183Rank3O. glumaepatulaAABritish Guiana
46W1184DRA004526W1184Rank3O. latifoliaCCDDPerennialSuriname
47W1185DRA004589W1185Rank2O. glumaepatulaAAPerennialSuriname
48W1187DRA004589W1187Rank2O. glumaepatulaAABrazil
49W1189DRA004589W1189Rank3O. glumaepatulaAAPerennialBrazil
50W1191DRA004589W1191Rank3O. glumaepatulaAAAnnualBrazil
51W1194DRA004527W1194Rank1O. grandiglumisCCDDPerennialBrazil
52W1196DRA004589W1196Rank2O. glumaepatulaAAColombia
53W1197DRA004526W1197Rank1O. latifoliaCCDDPerennialColombia
54W1200DRA004552W1200Rank3O. officinalisCCPerennialPhilippines
55W1213DRA004586W1213Rank1O. minutaBBCCPerennialPhilippines
56W1215DRA004507W1215Rank2O. longiglumisHHJJPerennialDutch New Guinea (Indonesia)
57W1220DRA004507W1220Rank1O. longiglumisHHJJPerennialDutch New Guinea (Indonesia)
58W1224DRA004507W1224Rank2O. longiglumisHHJJPerennialDutch New Guinea (Indonesia)
59W1228DRA004507W1228Rank2O. longiglumisHHJJPerennialDutch New Guinea (Indonesia)
60W1229DRA004507W1229Rank1O. longiglumisHHJJPerennialDutch New Guinea (Indonesia)
61W1232DRA004591W1232Rank3O. longistaminataAAPerennialTanganyika
62W1247DRA004527W1247Rank3O. grandiglumisCCDDPerennialBrazil
63W1252DRA004552W1252Rank3O. officinalisCCPerennialMalaysia
64W1270DRA004552W1270Rank3O. officinalisCCPerennialBrunei
65W1291DRA004552W1291Rank3O. officinalisCCPerennialLocal name : Padi KujangIndonesia
66W1297DRA004590W1297Rank2O. meridionalisAAAnnualAustralia
67W1300DRA004590W1300Rank3O. meridionalisAAAnnualAustralia
68W1301DRA004552W1301Rank3O. officinalisCCPerennialMalaysia
69W1302DRA004552W1302Rank2O. officinalisCCPerennialPhilippines
70W1308DRA004552W1308Rank3O. officinalisCCPerennialPhilippines
71W1315DRA004552W1315Rank3O. officinalisCCPerennialPhilippines
72W1319DRA004585W1319Rank2O. minutaBBCCPerennialPhilippines
73W1323DRA004585W1323Rank2O. minutaBBCCPhilippines
74W1328DRA004586W1328Rank2O. minutaBBCCPerennialPhilippines
75W1329DRA004586W1329Rank2O. minutaBBCCPerennialPhilippines
76W1331DRA004586W1331Rank1O. minutaBBCCPerennialPhilippines
77W1342DRA004586W1342Rank3O. minutaBBCCPerennialPhilippines
78W1344DRA004586W1344Rank3O. minutaBBCCPerennialPhilippines
79W1348DRA004510W1348Rank2O. meyerianaGGMalaysia
80W1352DRA004510W1352Rank2O. meyerianaGGMalaysia
81W1356DRA004510W1356Rank1O. meyerianaGGPerennialMalaysia
82W1360DRA004510W1360Rank2O. meyerianaGGMalaysia
83W1361DRA004552W1361Rank1O. officinalisCCPerennialMalaysia
84W1401DRA004336W1401Rank1O. brachyanthaFFSierra Leone
85W1402DRA004336W1402Rank3O. brachyanthaFFSierra Leone
86W1403DRA004336W1403Rank3O. brachyanthaFFSierra Leone
87W1404DRA004336W1404Rank3O. brachyanthaFFSierra Leone
88W1405DRA004336W1405Rank3O. brachyanthaFFSierra Leone
89W1407(B)DRA004336W1407(B)Rank2O. brachyanthaFFMali
90W1408DRA004587W1408Rank2O. punctata (4X)BBCCPerennialNigeria
91W1409DRA004587W1409Rank3O. punctata (4X)BBCCPerennialNigeria
92W1410DRA004588W1410Rank3O. barthiiAAAnnualSierra Leone
93W1413DRA004591W1413Rank1O. longistaminataAAPerennialSierra Leone
94W1416DRA004588W1416Rank3O. barthiiAAAnnualLocal name : Yerr-yerrSierra Leone
95W1420DRA004591W1420Rank3O. longistaminataAAPerennialMali
96W1423DRA004591W1423Rank3O. longistaminataAAMali
97W1443(A)DRA004588W1443(A)Rank3O. barthiiAAAnnualMali
98W1444DRA004591W1444Rank3O. longistaminataAAPerennialIvory Coast
99W1448DRA004591W1448Rank3O. longistaminataAAPerennialIvory Coast
100W1454(B)DRA004591W1454(B)Rank3O. longistaminataAAPerennialUpper Volta (Burkina Faso)
101W1460DRA004591W1460Rank3O. longistaminataAAPerennialDahomey
102W1465DRA004591W1465Rank3O. longistaminataAANigeria
103W1467DRA004588W1467Rank3O. barthiiAAAnnualCameroun
104W1473DRA004588W1473Rank3O. barthiiAAAnnualTchad (=Chad)
105W1476DRA004527W1476Rank2O. grandiglumisCCDDPerennialBrazil
106W1477DRA004589W1477Rank3O. glumaepatulaAAPerennialBrazil
107W1480(B)DRA004527W1480(B)Rank2O. grandiglumisCCDDBrazil
108W1483DRA004527W1483Rank3O. grandiglumisCCDDBrazil
109W1504DRA004591W1504Rank3O. longistaminataAAPerennialTanganyika
110W1508DRA004591W1508Rank1O. longistaminataAAPerennialMadagascar
111W1514DRA004491W1514Rank1O. punctata (2X)BBPerennialKenya
112W1515DRA004491W1515Rank3O. punctata (2X)BBPerennialTanganyika
113W1519DRA004551W1519Rank2O. eichingeriCCPerennialUganda
114W1522DRA004551W1522Rank2O. eichingeriCCUganda
115W1526DRA004551W1526Rank3O. eichingeriCCAnnual?Uganda
116W1527DRA004551W1527Rank1O. eichingeriCCPerennialUganda
117W1539DRA004526W1539Rank3O. latifoliaCCDDArgentina
118W1540DRA004591W1540Rank2O. longistaminataAACongo
119W1551DRA005599W1551Rank3O. rufipogonAAThailand
120W1564DRA004587W1564Rank3O. punctata (4X)BBCCNigeria
121W1573DRA004591W1573Rank3O. longistaminataAANigeria
122W1574DRA004588W1574Rank3O. barthiiAAAnnualNigeria
123W1577DRA004491W1577Rank3O. punctata (2X)BBNigeria
124W1582DRA004491W1582Rank3O. punctata (2X)BBTchad (=Chad)
125W1583DRA004588W1583Rank3O. barthiiAAAnnualTchad (=Chad)
126W1586DRA004491W1586Rank3O. punctata (2X)BBTchad (=Chad)
127W1588DRA004588W1588Rank1O. barthiiAAAnnualCameroun
128W1590DRA004491W1590Rank2O. punctata (2X)BBCameroun
129W1592DRA004491W1592Rank3O. punctata (2X)BBCameroun
130W1593DRA004491W1593Rank3O. punctata (2X)BBNigeria
131W1605DRA004588W1605Rank3O. barthiiAAAnnualNigeria
132W1624DRA004591W1624Rank2O. longistaminataAACameroun
133W1625DRA004590W1625Rank1O. meridionalisAAAustralia
134W1627DRA004590W1627Rank2O. meridionalisAAAustralia
135W1628DRA004524W1628Rank1O. australiensisEEAustralia
136W1631DRA004590W1631Rank3O. meridionalisAAAustralia
137W1632DRA004524W1632Rank2O. australiensisEEAustralia
138W1635DRA004590W1635Rank1O. meridionalisAAAustralia
139W1638DRA004590W1638Rank3O. meridionalisAAAustralia
140W1642DRA004588W1642Rank3O. barthiiAAAnnualBotswana
141W1643DRA004588W1643Rank3O. barthiiAAAnnualBotswana
142W1646DRA004588W1646Rank2O. barthiiAAAnnualTanzania
143W1650DRA004591W1650Rank3O. longistaminataAATanzania
144W1669DRA005599W1669Rank3O. rufipogonAAIndia
145W1681DRA005599W1681Rank3O. rufipogonAAIndia
146W1702DRA004588W1702Rank3O. barthiiAAAnnualMali
147W1703DRA004336W1703Rank3O. brachyanthaFFMali
148W1705DRA004336W1705Rank3O. brachyanthaFFMali
149W1706DRA004336W1706Rank2O. brachyanthaFFTchad (=Chad)
150W1708DRA004336W1708Rank3O. brachyanthaFFCameroun
151W1711DRA004336W1711Rank1O. brachyanthaFFCameroun
152W1712DRA004336W1712Rank3O. brachyanthaFFCameroun
153W1715DRA005599W1715Rank3O. rufipogonAAChina
154W1805DRA004466W1805Rank1O. rhizomatisCCSri Lanka
155W1807DRA005599W1807Rank2O. rufipogonAASri Lanka
156W1808DRA004436W1808Rank3O. rhizomatisCCSri Lanka
157W1814DRA004552W1814Rank2O. officinalisCCSri Lanka
158W1830DRA004552W1830Rank1O. officinalisCC
159W1866DRA005599W1866Rank1O. rufipogonAAThailand
160W1921DRA005599W1921Rank1O. rufipogonAAThailand
161W1930DRA004552W1930Rank3O. officinalisCCThailand
162W1945DRA005599W1945Rank2O. rufipogonAA
163W1962DRA005599W1962Rank4O. rufipogonAAChina
164W2003DRA005599W2003Rank1O. rufipogonAAIndia
165W2035DRA004508W2035Rank2O. ridleyiHHJJThailand
166W2051DRA005599W2051Rank2O. rufipogonAABangladesh
167W2068DRA004510W2068Rank2O. meyerianaGG
168W2069DRA004590W2069Rank2O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
169W2071DRA004590W2071Rank3O. meridionalisAAAustralia
170W2072DRA004524W2072Rank3O. australiensisEEAustralia
171W2077DRA005599W2077Rank3O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
172W2078DRA005599W2078Rank2O. rufipogonAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
173W2079DRA004590W2079Rank2O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
174W2080DRA004590W2080Rank3O. meridionalisAAAustralia
175W2081DRA004590W2081Rank3O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
176W2082DRA004524W2082Rank3O. australiensisEEAustralia
177W2084DRA004524W2084Rank3O. australiensisEEAustralia
178W2086DRA004524W2086Rank2O. australiensisEEAustralia
179W2100DRA005599W2100Rank3O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
180W2103DRA004590W2103Rank2O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
181W2104DRA004524W2104Rank2O. australiensisEEAustralia
182W2105DRA004590W2105Rank3O. meridionalisAAAustralia
183W2109DRA005599W2109Rank3O. rufipogonAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
184W2112DRA004590W2112Rank3O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
185W2114DRA004590W2114Rank4O. rufipogon/O. meridionalisAAAustralia
186W2116DRA004590W2116Rank3O. meridionalisAAStrains characterized by p-SINE1 insertion polymorphism (Xu et al. Identification and characterization of Australian wild rice strains of Oryza meridionalis and Oryza rufipogon by SINE insertion polymorphism. GGS)Australia
187W2117DRA004590W2117Rank4O. rufipogon/O. meridionalisAAAustralia
188W2140DRA004589W2140Rank3O. glumaepatulaAABrazil
189W2145DRA004589W2145Rank1O. glumaepatulaAABrazil
190W2149DRA004589W2149Rank3O. glumaepatulaAABrazil
191W2160DRA004589W2160Rank3O. glumaepatulaAABrazil
192W2165DRA004589W2165Rank3O. glumaepatulaAABrazil
193W2173DRA004589W2173Rank3O. glumaepatulaAABrazil
194W2184DRA004589W2184Rank3O. glumaepatulaAABrazil
195W2192DRA004589W2192Rank3O. glumaepatulaAABrazil
196W2199DRA004589W2199Rank1O. glumaepatulaAABrazil
197W2200DRA004526W2200Rank1O. latifoliaCCDDBrazil
198W2201DRA004589W2201Rank3O. glumaepatulaAABrazil
199W2203DRA004589W2203Rank3O. glumaepatulaAABrazil
200W2220DRA004527W2220Rank1O. grandiglumisCCDDBrazil
201W2263DRA005599W2263Rank2O. rufipogonAACambodia
202IRGC105715DRA005599
203IRGC105444DRA005599
204IRGC104038DRA004592O.glaberrima
205IRGC103777DRA004592O.glaberrima
206IRGC105668DRA004589O. glumaepatulaAA
207IRGC105908DRA005599
208C0492DRA004592O.glaberrima

36 Deep Sequenced Accessions List


36 deep NGS genome sequences comprised of thirty O. rufipogon accessions, two O. longistaminata accessions (W1413 and W1508) and four cultivated Oryza strains (Nipponbare, Guangluai-4, Nongken-58, Kasalath) are listed. NGS data of these accessions were mapped on the Nipponbare genome (IRGSP version 1.0). The variant list contains datasets of genome-wide SNP information for each accession.

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IDCultivar / NIG Wild Rice accessionSpeciesSubspecies / EcotypeSequence Read Archive accessionShigen
1Guangluai-4  
Oryza sativaindicaERA009070
2Kasalath  
Oryza sativaausDRA000968
3Nipponbare (NIG stock)  
Oryza sativajaponicaDRA000158
4Nongken-58  
Oryza sativajaponicaERA009071
5W0106  
O. rufipogonOr-IDRA000158Link
6W0120  
O. rufipogonOr-IIDRA000419Link
7W0137  
O. rufipogonOr-IIIDRA005599Link
8W0180  
O. rufipogonOr-IIDRA000419Link
9W0593  
O. rufipogonOr-IIIDRA000419Link
10W0630  
O. rufipogonOr-IDRA000419Link
11W1230  
O. rufipogonOr-IDRA000419Link
12W1236  
O. rufipogonOr-IIDRA000419Link
13W1413  
O. longistaminataN.D.DRA000031Link
14W1508  
O. longistaminataN.D.DRA000031Link
15W1551  
O. rufipogonOr-IDRA005599Link
16W1669  
O. rufipogonOr-IIIDRA005599Link
17W1681  
O. rufipogonOr-IDRA005599Link
18W1715  
O. rufipogonOr-IIDRA000419Link
19W1807  
O. rufipogonOr-IIIDRA005599Link
20W1866  
O. rufipogonOr-IDRA005599Link
21W1886  
O. rufipogonN.D.SRA106223Link
22W1921  
O. rufipogonOr-IDRA000158Link
23W1943  
O. rufipogonOr-IIIERA125029Link
24W1945  
O. rufipogonOr-IIIDRA005599Link
25W1962  
O. rufipogonN.D.DRA005599Link
26W1965  
O. rufipogonN.D.SRA106223Link
27W1976  
O. rufipogonOr-IISRA106223Link
28W1981  
O. rufipogonOr-IIDRA000419Link
29W2003  
O. rufipogonOr-IIIDRA005599Link
30W2051  
O. rufipogonOr-IIDRA005599Link
31W2057  
O. rufipogonOr-IIISRA106223Link
32W2078  
O. rufipogonOr-IIIDRA005599Link
33W2109  
O. rufipogonN.D.DRA005599Link
34W2114  
O. rufipogon/O. meridionalisN.D.DRA004590Link
35W2117  
O. rufipogon/O. meridionalisN.D.DRA004590Link
36W2263  
O. rufipogonOr-IDRA005599Link

SnpEff-based Variant Lists of deeper sequenced 17 accessions


Deeper sequenced 17 accessions are Kasalath, Guangluai-4, Nipponbare(NIG stock), Nongken-58, W0106, W0120, W0180, W0593, W0630, W1230, W1236, W1413, W1508, W1715, W1921, W1943 and W1981. (See "Release 1.0 contents" for details.)
The variant annotation list contains datasets of SNP information for each accession based on the latest reference Nipponbare genome, IRGSP version 1.0.

  • Choromosomes
    • chromsome 1 SNP List   
    • chromsome 2 SNP List   
    • chromsome 3 SNP List   
    • chromsome 4 SNP List   
    • chromsome 5 SNP List   
    • chromsome 6 SNP List   
    • chromsome 7 SNP List   
    • chromsome 8 SNP List   
    • chromsome 9 SNP List   
    • chromsome 10 SNP List   
    • chromsome 11 SNP List   
    • chromsome 12 SNP List   
  • Full data set
    • All SNP List   

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 SNPs of deeper sequenced 17 accessions

Download imputed SNPs of 446 O. rufipogon accessions