| Variant ID: vg0704183320 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 4183320 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.77, T: 0.22, others allele: 0.00, population size: 195. )
TTCTTGACCAAACTTAAGTTGTGCCCACACATACCGTATATTGGTTTATCCTAGTAAACACAACCAAGAATGAATTAACTTCACAATCCTGAACACATAT[C/T]
TATACAAGACAGCACATAAAATGTTTTATATTTATTTTAATAAATCCTGCATCTTCTTATAGCCAAATTATAAGAATGATTCTGTGTTGCTATATGTCCT
AGGACATATAGCAACACAGAATCATTCTTATAATTTGGCTATAAGAAGATGCAGGATTTATTAAAATAAATATAAAACATTTTATGTGCTGTCTTGTATA[G/A]
ATATGTGTTCAGGATTGTGAAGTTAATTCATTCTTGGTTGTGTTTACTAGGATAAACCAATATACGGTATGTGTGGGCACAACTTAAGTTTGGTCAAGAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 57.30% | 42.40% | 0.00% | 0.38% | NA |
| All Indica | 2759 | 95.70% | 4.00% | 0.00% | 0.33% | NA |
| All Japonica | 1512 | 0.80% | 98.90% | 0.00% | 0.26% | NA |
| Aus | 269 | 7.40% | 92.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.10% | 6.70% | 0.00% | 0.17% | NA |
| Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.00% | 1.50% | 0.00% | 0.44% | NA |
| Indica Intermediate | 786 | 94.30% | 5.20% | 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 | 35.60% | 58.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704183320 | C -> DEL | N | N | silent_mutation | Average:60.521; most accessible tissue: Callus, score: 77.247 | N | N | N | N |
| vg0704183320 | C -> T | LOC_Os07g08190.1 | downstream_gene_variant ; 1671.0bp to feature; MODIFIER | silent_mutation | Average:60.521; most accessible tissue: Callus, score: 77.247 | N | N | N | N |
| vg0704183320 | C -> T | LOC_Os07g08210.1 | downstream_gene_variant ; 1885.0bp to feature; MODIFIER | silent_mutation | Average:60.521; most accessible tissue: Callus, score: 77.247 | N | N | N | N |
| vg0704183320 | C -> T | LOC_Os07g08210.3 | downstream_gene_variant ; 1885.0bp to feature; MODIFIER | silent_mutation | Average:60.521; most accessible tissue: Callus, score: 77.247 | N | N | N | N |
| vg0704183320 | C -> T | LOC_Os07g08210.2 | downstream_gene_variant ; 1885.0bp to feature; MODIFIER | silent_mutation | Average:60.521; most accessible tissue: Callus, score: 77.247 | N | N | N | N |
| vg0704183320 | C -> T | LOC_Os07g08200.1 | intron_variant ; MODIFIER | silent_mutation | Average:60.521; most accessible tissue: Callus, score: 77.247 | N | N | N | N |