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Georg-August-Universität Göttingen
CiBreed

Overview for Oryza glaberrima (African rice)

Oryza glaberrima (African rice) is, besides the Asian rice (Oryza sativa), one of the two domesticated rice species. African rice was first domesticated and cultivated in West Africa about 3,000 years ago. Although it is lower-yielding compared to Asian rice, it has some beneficial characteristics such as resistance to many pests and diseases and tolerance to drought and infertile soils. Similar to Asian rice, African rice is a diploid type A genome with 12 chromosomes (excluding unmapped contigs or scaffolds) and a size of ~358 Mb. In agReg-SNPdb, we store 33,164 genes and 7,567,669 SNPs.


african_rice

Statistics

(Last updated on 08.02.2022)

Number of chromosomes 904
Number of genes 33,164
Number of SNPs 7,567,669

Click on a chromosome to download the data stored in agReg-SNPdb for the complete chromosome

Chromosome Number of SNPs Number of Genes
1 779,993 3,968
10 530,176 1,525
11 625,931 1,907
12 568,088 1,789
2 725,400 3,384
3 797,024 3,918
4 654,421 2,715
5 629,174 2,460
6 609,800 2,508
7 622,300 2,190
8 551,320 1,941
9 474,042 1,713
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Oglab07_unplaced158 0 5
Oglab07_unplaced159 0 34
Oglab07_unplaced160 0 14
Oglab07_unplaced161 0 17
Oglab08_unplaced005 0 1
Oglab08_unplaced019 0 1
Oglab08_unplaced020 0 1
Oglab08_unplaced024 0 3
Oglab08_unplaced025 0 16
Oglab08_unplaced026 0 2
Oglab08_unplaced036 0 1
Oglab08_unplaced046 0 1
Oglab08_unplaced052 0 3
Oglab08_unplaced053 0 1
Oglab08_unplaced059 0 3
Oglab08_unplaced063 0 2
Oglab08_unplaced064 0 3
Oglab08_unplaced066 0 2
Oglab08_unplaced067 0 1
Oglab08_unplaced068 0 2
Oglab08_unplaced071 0 2
Oglab08_unplaced073 0 1
Oglab08_unplaced075 0 15
Oglab08_unplaced076 0 2
Oglab08_unplaced087 0 13
Oglab08_unplaced089 0 1
Oglab08_unplaced090 0 3
Oglab08_unplaced092 0 53
Oglab08_unplaced095 0 4
Oglab08_unplaced109 0 1
Oglab08_unplaced115 0 7
Oglab08_unplaced138 0 226
Oglab08_unplaced143 0 12
Oglab08_unplaced145 0 2
Oglab08_unplaced149 0 1
Oglab08_unplaced151 0 1
Oglab09_unplaced005 0 5
Oglab09_unplaced007 0 14
Oglab09_unplaced012 0 4
Oglab09_unplaced015 0 9
Oglab09_unplaced018 0 4
Oglab09_unplaced022 0 7
Oglab09_unplaced023 0 2
Oglab09_unplaced024 0 1
Oglab09_unplaced026 0 9
Oglab09_unplaced028 0 11
Oglab09_unplaced029 0 3
Oglab09_unplaced038 0 2
Oglab09_unplaced039 0 2
Oglab09_unplaced041 0 2
Oglab09_unplaced042 0 4
Oglab09_unplaced049 0 1
Oglab09_unplaced051 0 1
Oglab09_unplaced055 0 5
Oglab09_unplaced057 0 1
Oglab09_unplaced059 0 4
Oglab09_unplaced060 0 1
Oglab09_unplaced061 0 6
Oglab09_unplaced063 0 1
Oglab09_unplaced064 0 1
Oglab09_unplaced065 0 1
Oglab09_unplaced098 0 1
Oglab09_unplaced099 0 1
Oglab09_unplaced103 0 1
Oglab10_unplaced003 0 1
Oglab10_unplaced005 0 2
Oglab10_unplaced006 0 1
Oglab10_unplaced012 0 5
Oglab10_unplaced015 0 10
Oglab10_unplaced016 0 24
Oglab10_unplaced017 0 8
Oglab10_unplaced023 0 2
Oglab10_unplaced026 0 8
Oglab10_unplaced031 0 1
Oglab10_unplaced032 0 1
Oglab10_unplaced034 0 2
Oglab10_unplaced035 0 1
Oglab10_unplaced042 0 3
Oglab10_unplaced044 0 3
Oglab10_unplaced045 0 5
Oglab10_unplaced047 0 4
Oglab10_unplaced048 0 2
Oglab10_unplaced050 0 2
Oglab10_unplaced054 0 2
Oglab10_unplaced058 0 4
Oglab10_unplaced061 0 1
Oglab10_unplaced062 0 1
Oglab10_unplaced064 0 1
Oglab10_unplaced066 0 2
Oglab10_unplaced070 0 1
Oglab10_unplaced075 0 6
Oglab10_unplaced076 0 1
Oglab10_unplaced077 0 3
Oglab10_unplaced078 0 1
Oglab10_unplaced079 0 1
Oglab10_unplaced080 0 1
Oglab10_unplaced083 0 1
Oglab10_unplaced084 0 12
Oglab10_unplaced090 0 1
Oglab10_unplaced091 0 5
Oglab10_unplaced093 0 2
Oglab10_unplaced094 0 1
Oglab10_unplaced097 0 1
Oglab10_unplaced098 0 1
Oglab11_unplaced006 0 63
Oglab11_unplaced007 0 4
Oglab11_unplaced015 0 6
Oglab11_unplaced016 0 14
Oglab11_unplaced017 0 38
Oglab11_unplaced030 0 2
Oglab11_unplaced040 0 3
Oglab11_unplaced043 0 3
Oglab11_unplaced045 0 4
Oglab11_unplaced046 0 2
Oglab11_unplaced048 0 2
Oglab11_unplaced050 0 1
Oglab11_unplaced052 0 1
Oglab11_unplaced053 0 1
Oglab11_unplaced060 0 3
Oglab11_unplaced062 0 21
Oglab11_unplaced063 0 1
Oglab11_unplaced068 0 10
Oglab11_unplaced071 0 1
Oglab11_unplaced072 0 1
Oglab11_unplaced081 0 7
Oglab11_unplaced084 0 6
Oglab11_unplaced085 0 2
Oglab11_unplaced089 0 1
Oglab11_unplaced091 0 3
Oglab11_unplaced094 0 22
Oglab11_unplaced097 0 2
Oglab11_unplaced100 0 9
Oglab11_unplaced103 0 3
Oglab11_unplaced104 0 3
Oglab11_unplaced107 0 1
Oglab11_unplaced108 0 1
Oglab11_unplaced111 0 1
Oglab11_unplaced114 0 2
Oglab11_unplaced116 0 2
Oglab11_unplaced122 0 1
Oglab11_unplaced123 0 1
Oglab11_unplaced124 0 1
Oglab11_unplaced125 0 3
Oglab11_unplaced138 0 2
Oglab11_unplaced140 0 1
Oglab11_unplaced141 0 1
Oglab11_unplaced142 0 23
Oglab11_unplaced144 0 10
Oglab11_unplaced145 0 1
Oglab11_unplaced146 0 1
Oglab11_unplaced148 0 1
Oglab11_unplaced149 0 3
Oglab11_unplaced150 0 2
Oglab11_unplaced154 0 1
Oglab11_unplaced155 0 3
Oglab11_unplaced160 0 1
Oglab12_unplaced003 0 3
Oglab12_unplaced005 0 3
Oglab12_unplaced010 0 1
Oglab12_unplaced044 0 1
Oglab12_unplaced045 0 28
Oglab12_unplaced047 0 1
Oglab12_unplaced051 0 3
Oglab12_unplaced052 0 1
Oglab12_unplaced060 0 5
Oglab12_unplaced062 0 1
Oglab12_unplaced064 0 1
Oglab12_unplaced066 0 2
Oglab12_unplaced082 0 1
Oglab12_unplaced083 0 14
Oglab12_unplaced084 0 1
Oglab12_unplaced087 0 5
Oglab12_unplaced089 0 2
Oglab12_unplaced090 0 2
Oglab12_unplaced093 0 2
Oglab12_unplaced100 0 1
Oglab12_unplaced101 0 2
Oglab12_unplaced102 0 11
Oglab12_unplaced104 0 4
Oglab12_unplaced117 0 2
Oglab12_unplaced121 0 3
Oglab12_unplaced122 0 2
Oglab12_unplaced125 0 1
Oglab12_unplaced127 0 1
Oglab12_unplaced130 0 1
Oglab12_unplaced132 0 4
Oglab12_unplaced134 0 1
Oglab12_unplaced138 0 2
Oglab12_unplaced140 0 4
Oglab12_unplaced142 0 7
Oglab12_unplaced153 0 1
Oglab12_unplaced154 0 1
Oglab12_unplaced155 0 3
Oglab12_unplaced156 0 30
Oglab12_unplaced158 0 1
Oglab12_unplaced160 0 1
Oglab12_unplaced162 0 42
Oglab12_unplaced176 0 13
Oglab12_unplaced178 0 2
Oglab12_unplaced184 0 17
Oglab12_unplaced185 0 2
Oglab12_unplaced187 0 1
Oglab12_unplaced192 0 1



Distribution of rSNPs relative to the TSS

SNP distance to TSS african rice
Distribution of SNPs around the TSS of african rice. The upper plot shows the counts for the whole promoter region (-7.5 kb to +2.5 kb) in 500 bp intervals. The enlargement shows the proximal promoter region (-750 bp to +250 bp) in 50 bp intervals. The red asterisk annotates the position of the TSS.


Input data (Ensembl Plants)

Plant Assembly version Download links
Oryza glaberrima (African rice) Oryza_glaberrima_V1 Reference genome
SNPs
Genes
(downloaded on 08 November 2021)