| Variant ID: vg0804463714 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 4463714 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 107. )
ATTTGAATACAAATTCTCTGAGTTTACCGATAAGCTTGTGAAAACCGGTCGGCTTTGGCGAAATTCCGAGCGAAATCATCGAAATTTCAATCAATAACTA[T/G]
AAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATTCGTTATTCTTTTCTTTCCTATTGTAAATTTCAGTAAATACATGGAATACATCAGTTTTTTTG
CAAAAAAACTGATGTATTCCATGTATTTACTGAAATTTACAATAGGAAAGAAAAGAATAACGAATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTT[A/C]
TAGTTATTGATTGAAATTTCGATGATTTCGCTCGGAATTTCGCCAAAGCCGACCGGTTTTCACAAGCTTATCGGTAAACTCAGAGAATTTGTATTCAAAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.30% | 0.60% | 0.51% | 64.64% | NA |
| All Indica | 2759 | 4.50% | 0.40% | 0.47% | 94.60% | NA |
| All Japonica | 1512 | 95.00% | 0.20% | 0.07% | 4.70% | NA |
| Aus | 269 | 2.20% | 4.50% | 2.97% | 90.33% | NA |
| Indica I | 595 | 6.60% | 0.00% | 0.50% | 92.94% | NA |
| Indica II | 465 | 6.00% | 0.00% | 0.43% | 93.55% | NA |
| Indica III | 913 | 1.80% | 0.70% | 0.11% | 97.48% | NA |
| Indica Intermediate | 786 | 5.30% | 0.60% | 0.89% | 93.13% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
| Tropical Japonica | 504 | 88.70% | 0.60% | 0.00% | 10.71% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 1.04% | 82.29% | NA |
| Intermediate | 90 | 40.00% | 1.10% | 1.11% | 57.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463714 | T -> G | LOC_Os08g07900.1 | upstream_gene_variant ; 3491.0bp to feature; MODIFIER | silent_mutation | Average:14.719; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463714 | T -> G | LOC_Os08g07910.1 | upstream_gene_variant ; 2593.0bp to feature; MODIFIER | silent_mutation | Average:14.719; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463714 | T -> G | LOC_Os08g07930.1 | upstream_gene_variant ; 2315.0bp to feature; MODIFIER | silent_mutation | Average:14.719; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463714 | T -> G | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.719; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463714 | T -> DEL | N | N | silent_mutation | Average:14.719; most accessible tissue: Callus, score: 29.336 | N | N | N | N |