| Variant ID: vg0804463806 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr08 | Position: 4463806 |
| Reference Allele: G | Alternative Allele: T,GT |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 86. )
AATAACTATAAATAGAGGTAAACTAAAATTGTTTTCCTTTTTTAATTCGTTATTCTTTTCTTTCCTATTGTAAATTTCAGTAAATACATGGAATACATCA[G/T,GT]
TTTTTTTGAAAATTTATATCCCAATAGGTTCTATGAATATCATACTATTTATAAGATTTTATTTGATTTTTTCCTTTTTTATCAATTTAAATTTGAATTT
AAATTCAAATTTAAATTGATAAAAAAGGAAAAAATCAAATAAAATCTTATAAATAGTATGATATTCATAGAACCTATTGGGATATAAATTTTCAAAAAAA[C/A,AC]
TGATGTATTCCATGTATTTACTGAAATTTACAATAGGAAAGAAAAGAATAACGAATTAAAAAAGGAAAACAATTTTAGTTTACCTCTATTTATAGTTATT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 33.70% | 0.90% | 0.66% | 64.68% | GT: 0.04% |
| All Indica | 2759 | 4.00% | 1.50% | 0.40% | 94.13% | NA |
| All Japonica | 1512 | 94.40% | 0.00% | 0.46% | 4.96% | GT: 0.13% |
| Aus | 269 | 1.10% | 0.40% | 3.35% | 95.17% | NA |
| Indica I | 595 | 6.20% | 2.70% | 0.50% | 90.59% | NA |
| Indica II | 465 | 5.60% | 1.90% | 0.43% | 92.04% | NA |
| Indica III | 913 | 1.40% | 0.50% | 0.11% | 97.92% | NA |
| Indica Intermediate | 786 | 4.30% | 1.40% | 0.64% | 93.64% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.78% | 1.69% | NA |
| Tropical Japonica | 504 | 88.50% | 0.00% | 0.00% | 11.11% | GT: 0.40% |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 15.60% | 1.00% | 3.12% | 80.21% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0804463806 | G -> GT | LOC_Os08g07900.1 | upstream_gene_variant ; 3584.0bp to feature; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> GT | LOC_Os08g07910.1 | upstream_gene_variant ; 2686.0bp to feature; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> GT | LOC_Os08g07930.1 | upstream_gene_variant ; 2222.0bp to feature; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> GT | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> T | LOC_Os08g07900.1 | upstream_gene_variant ; 3583.0bp to feature; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> T | LOC_Os08g07910.1 | upstream_gene_variant ; 2685.0bp to feature; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> T | LOC_Os08g07930.1 | upstream_gene_variant ; 2223.0bp to feature; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> T | LOC_Os08g07920.1 | intron_variant ; MODIFIER | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |
| vg0804463806 | G -> DEL | N | N | silent_mutation | Average:14.644; most accessible tissue: Callus, score: 29.336 | N | N | N | N |