| Variant ID: vg0811599981 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599981 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, C: 0.06, others allele: 0.00, population size: 47. )
GTGAGTGAAAACTCGCCTTGGGAGATGGGAGAATGAATACGGCCGCGGTGGGCGCGGGGACGAACCTGCGGGGAGGTCGGCTAAACGACCACCTCGGGGG[T/C]
GAGATGAGGTTCCCCCGGCATGGCACAATCCCCCCCATCTTGCGGGGCCGTTTCTTCTTTCGCTCCCCCTCGGGCTGCGGCGTCGGCACGGCACCCTCCG
CGGAGGGTGCCGTGCCGACGCCGCAGCCCGAGGGGGAGCGAAAGAAGAAACGGCCCCGCAAGATGGGGGGGATTGTGCCATGCCGGGGGAACCTCATCTC[A/G]
CCCCCGAGGTGGTCGTTTAGCCGACCTCCCCGCAGGTTCGTCCCCGCGCCCACCGCGGCCGTATTCATTCTCCCATCTCCCAAGGCGAGTTTTCACTCAC
| 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 | 2.90% | 0.10% | 3.34% | 93.59% | NA |
| All Indica | 2759 | 0.20% | 0.30% | 3.99% | 95.54% | NA |
| All Japonica | 1512 | 8.60% | 0.00% | 2.31% | 89.09% | NA |
| Aus | 269 | 0.00% | 0.00% | 4.46% | 95.54% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.67% | 99.33% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.65% | 99.35% | NA |
| Indica III | 913 | 0.30% | 0.80% | 9.53% | 89.38% | NA |
| Indica Intermediate | 786 | 0.40% | 0.00% | 2.04% | 97.58% | NA |
| Temperate Japonica | 767 | 11.10% | 0.00% | 4.04% | 84.88% | NA |
| Tropical Japonica | 504 | 5.00% | 0.00% | 0.60% | 94.44% | NA |
| Japonica Intermediate | 241 | 8.30% | 0.00% | 0.41% | 91.29% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 1.11% | 96.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599981 | T -> C | LOC_Os08g19380.1 | upstream_gene_variant ; 4058.0bp to feature; MODIFIER | silent_mutation | Average:11.011; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599981 | T -> C | LOC_Os08g19410.1 | upstream_gene_variant ; 3252.0bp to feature; MODIFIER | silent_mutation | Average:11.011; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599981 | T -> C | LOC_Os08g19390.1 | downstream_gene_variant ; 1706.0bp to feature; MODIFIER | silent_mutation | Average:11.011; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599981 | T -> C | LOC_Os08g19400.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.011; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |
| vg0811599981 | T -> DEL | N | N | silent_mutation | Average:11.011; most accessible tissue: Zhenshan97 panicle, score: 20.424 | N | N | N | N |