| Variant ID: vg0609017794 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 9017794 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 227. )
TTACACGTGAGGAAGATGTGTCTTGTGGGTAAAGATGTACACCTCTGATCAGAGTAAAACCTATTCGAATAGCCGCGCCCTCGGTTATGGGCAAGCCGAG[C/G]
AATGTACCCAAGTTAGTGTTTTAATTCTTAAAACCTGCTTAACGACTAAAATGTGGAATGGTTGGCCTGGGTTGGCTTGGGACGAGCTGGGACCCAGGGT
ACCCTGGGTCCCAGCTCGTCCCAAGCCAACCCAGGCCAACCATTCCACATTTTAGTCGTTAAGCAGGTTTTAAGAATTAAAACACTAACTTGGGTACATT[G/C]
CTCGGCTTGCCCATAACCGAGGGCGCGGCTATTCGAATAGGTTTTACTCTGATCAGAGGTGTACATCTTTACCCACAAGACACATCTTCCTCACGTGTAA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.60% | 0.40% | 10.35% | 40.58% | NA |
| All Indica | 2759 | 58.80% | 0.00% | 7.72% | 33.53% | NA |
| All Japonica | 1512 | 36.60% | 1.40% | 12.57% | 49.40% | NA |
| Aus | 269 | 27.10% | 0.00% | 13.38% | 59.48% | NA |
| Indica I | 595 | 57.80% | 0.00% | 2.02% | 40.17% | NA |
| Indica II | 465 | 78.30% | 0.00% | 8.17% | 13.55% | NA |
| Indica III | 913 | 43.80% | 0.00% | 11.72% | 44.47% | NA |
| Indica Intermediate | 786 | 65.30% | 0.00% | 7.12% | 27.61% | NA |
| Temperate Japonica | 767 | 66.50% | 2.70% | 5.87% | 24.90% | NA |
| Tropical Japonica | 504 | 3.20% | 0.00% | 19.44% | 77.38% | NA |
| Japonica Intermediate | 241 | 11.60% | 0.00% | 19.50% | 68.88% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 35.42% | 59.38% | NA |
| Intermediate | 90 | 50.00% | 0.00% | 17.78% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0609017794 | C -> G | LOC_Os06g15870.1 | upstream_gene_variant ; 3179.0bp to feature; MODIFIER | silent_mutation | Average:29.745; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |
| vg0609017794 | C -> G | LOC_Os06g15900.1 | upstream_gene_variant ; 3620.0bp to feature; MODIFIER | silent_mutation | Average:29.745; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |
| vg0609017794 | C -> G | LOC_Os06g15890.1 | downstream_gene_variant ; 1554.0bp to feature; MODIFIER | silent_mutation | Average:29.745; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |
| vg0609017794 | C -> G | LOC_Os06g15880.1 | intron_variant ; MODIFIER | silent_mutation | Average:29.745; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |
| vg0609017794 | C -> DEL | N | N | silent_mutation | Average:29.745; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |