| Variant ID: vg0234179980 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34179980 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 119. )
ATCTCAAGTATATTATCCAACAGCTAATTTAATTTTGCATAATATTCTTGAAATTGCCACTTTGTTGAAAGAGTATGAAAATGATGACCTTTTAATGCCC[G/A]
TTGTCTTTAATATGAAACAAAAATATCTTAAATATTGGAAAGACATCCCCATGTTGTATTCTTTTGCATTTATTCTTGATCCTAGGGGAAAATTACGGGG
CCCCGTAATTTTCCCCTAGGATCAAGAATAAATGCAAAAGAATACAACATGGGGATGTCTTTCCAATATTTAAGATATTTTTGTTTCATATTAAAGACAA[C/T]
GGGCATTAAAAGGTCATCATTTTCATACTCTTTCAACAAAGTGGCAATTTCAAGAATATTATGCAAAATTAAATTAGCTGTTGGATAATATACTTGAGAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.80% | 0.20% | 22.24% | 56.75% | NA |
| All Indica | 2759 | 0.70% | 0.30% | 19.14% | 79.81% | NA |
| All Japonica | 1512 | 61.30% | 0.10% | 31.08% | 7.54% | NA |
| Aus | 269 | 1.10% | 0.00% | 4.83% | 94.05% | NA |
| Indica I | 595 | 0.00% | 0.50% | 14.29% | 85.21% | NA |
| Indica II | 465 | 1.70% | 0.00% | 9.25% | 89.03% | NA |
| Indica III | 913 | 0.80% | 0.70% | 27.71% | 70.87% | NA |
| Indica Intermediate | 786 | 0.60% | 0.00% | 18.70% | 80.66% | NA |
| Temperate Japonica | 767 | 47.70% | 0.00% | 41.20% | 11.08% | NA |
| Tropical Japonica | 504 | 76.40% | 0.20% | 21.63% | 1.79% | NA |
| Japonica Intermediate | 241 | 73.00% | 0.00% | 18.67% | 8.30% | NA |
| VI/Aromatic | 96 | 10.40% | 0.00% | 16.67% | 72.92% | NA |
| Intermediate | 90 | 25.60% | 0.00% | 26.67% | 47.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234179980 | G -> A | LOC_Os02g55840.1 | upstream_gene_variant ; 2105.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179980 | G -> A | LOC_Os02g55840.2 | upstream_gene_variant ; 2105.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179980 | G -> A | LOC_Os02g55840.5 | upstream_gene_variant ; 2105.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179980 | G -> A | LOC_Os02g55840.4 | upstream_gene_variant ; 2105.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179980 | G -> A | LOC_Os02g55840.3 | upstream_gene_variant ; 2105.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179980 | G -> A | LOC_Os02g55840.6 | upstream_gene_variant ; 2107.0bp to feature; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179980 | G -> A | LOC_Os02g55830.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0234179980 | G -> DEL | N | N | silent_mutation | Average:4.505; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |