| Variant ID: vg0704183421 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4183421 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 241. )
TATACAAGACAGCACATAAAATGTTTTATATTTATTTTAATAAATCCTGCATCTTCTTATAGCCAAATTATAAGAATGATTCTGTGTTGCTATATGTCCT[A/G]
TTAAACACGACAGAATAAACCTTCATGGGTTGCTCATGGGAAACACAATTGAGAAAATACCGTAAACTGCAATGCAAAGAGGACATTAGAGAATCACCTC
GAGGTGATTCTCTAATGTCCTCTTTGCATTGCAGTTTACGGTATTTTCTCAATTGTGTTTCCCATGAGCAACCCATGAAGGTTTATTCTGTCGTGTTTAA[T/C]
AGGACATATAGCAACACAGAATCATTCTTATAATTTGGCTATAAGAAGATGCAGGATTTATTAAAATAAATATAAAACATTTTATGTGCTGTCTTGTATA
| 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 | 57.80% | 41.80% | 0.02% | 0.38% | NA |
| All Indica | 2759 | 95.80% | 3.80% | 0.04% | 0.33% | NA |
| All Japonica | 1512 | 0.80% | 98.90% | 0.00% | 0.26% | NA |
| Aus | 269 | 13.80% | 86.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.10% | 6.60% | 0.17% | 0.17% | NA |
| Indica II | 465 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.10% | 1.40% | 0.00% | 0.44% | NA |
| Indica Intermediate | 786 | 94.40% | 5.10% | 0.00% | 0.51% | NA |
| Temperate Japonica | 767 | 0.90% | 99.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 0.60% | 98.80% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 0.80% | 98.80% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 40.00% | 54.40% | 0.00% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0704183421 | A -> DEL | N | N | silent_mutation | Average:65.039; most accessible tissue: Zhenshan97 young leaf, score: 85.364 | N | N | N | N |
| vg0704183421 | A -> G | LOC_Os07g08190.1 | downstream_gene_variant ; 1772.0bp to feature; MODIFIER | silent_mutation | Average:65.039; most accessible tissue: Zhenshan97 young leaf, score: 85.364 | N | N | N | N |
| vg0704183421 | A -> G | LOC_Os07g08210.1 | downstream_gene_variant ; 1784.0bp to feature; MODIFIER | silent_mutation | Average:65.039; most accessible tissue: Zhenshan97 young leaf, score: 85.364 | N | N | N | N |
| vg0704183421 | A -> G | LOC_Os07g08210.3 | downstream_gene_variant ; 1784.0bp to feature; MODIFIER | silent_mutation | Average:65.039; most accessible tissue: Zhenshan97 young leaf, score: 85.364 | N | N | N | N |
| vg0704183421 | A -> G | LOC_Os07g08210.2 | downstream_gene_variant ; 1784.0bp to feature; MODIFIER | silent_mutation | Average:65.039; most accessible tissue: Zhenshan97 young leaf, score: 85.364 | N | N | N | N |
| vg0704183421 | A -> G | LOC_Os07g08200.1 | intron_variant ; MODIFIER | silent_mutation | Average:65.039; most accessible tissue: Zhenshan97 young leaf, score: 85.364 | N | N | N | N |