| Variant ID: vg0804463131 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4463131 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.64, A: 0.36, others allele: 0.00, population size: 47. )
TCGTATTTGATCCTAGATAGATATAGCAGATGCTTACATGGTCTAAGTAACATTCTTTGATAAGGTTTAATGCATATAAATATTGCATCAGTTTTTTTTT[A/T]
AAAAAAAAATTCTTCAATTGTTGTGATATATGCGCCCCAACCGATTTGAACTCTCAATGTAGGACTAATATATTCCCGGGTATTATGTTCACCTCCATTA
TAATGGAGGTGAACATAATACCCGGGAATATATTAGTCCTACATTGAGAGTTCAAATCGGTTGGGGCGCATATATCACAACAATTGAAGAATTTTTTTTT[T/A]
AAAAAAAAACTGATGCAATATTTATATGCATTAAACCTTATCAAAGAATGTTACTTAGACCATGTAAGCATCTGCTATATCTATCTAGGATCAAATACGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 31.80% | 1.90% | 1.95% | 64.35% | NA |
| All Indica | 2759 | 2.30% | 2.20% | 1.23% | 94.31% | NA |
| All Japonica | 1512 | 91.40% | 2.00% | 1.79% | 4.83% | NA |
| Aus | 269 | 2.60% | 0.00% | 7.43% | 89.96% | NA |
| Indica I | 595 | 2.20% | 4.90% | 1.51% | 91.43% | NA |
| Indica II | 465 | 4.70% | 1.50% | 1.51% | 92.26% | NA |
| Indica III | 913 | 0.40% | 0.80% | 0.66% | 98.14% | NA |
| Indica Intermediate | 786 | 3.10% | 2.20% | 1.53% | 93.26% | NA |
| Temperate Japonica | 767 | 91.50% | 3.80% | 3.26% | 1.43% | NA |
| Tropical Japonica | 504 | 88.50% | 0.20% | 0.20% | 11.11% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 12.50% | 2.10% | 8.33% | 77.08% | NA |
| Intermediate | 90 | 41.10% | 0.00% | 3.33% | 55.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463131 | A -> T | LOC_Os08g07900.1 | upstream_gene_variant ; 2908.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463131 | A -> T | LOC_Os08g07910.1 | upstream_gene_variant ; 2010.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463131 | A -> T | LOC_Os08g07930.1 | upstream_gene_variant ; 2898.0bp to feature; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463131 | A -> T | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |
| vg0804463131 | A -> DEL | N | N | silent_mutation | Average:10.026; most accessible tissue: Callus, score: 47.315 | N | N | N | N |