| Variant ID: vg0811599207 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599207 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
CAGGGTCCCTGGCCTGGTAGCTTGCCAGTACGAGCTCCACCGCCCCCCGGGCGAGGTCCCTCGAGGATGACTTGATCGTCTCCTCGAGCTCCTCGGGGAG[C/T]
CGCTTGAGGGTCCCGGCCATCTCTGAGAGGCGCTGGGCGAGGCCCCCCTGGTTGGCGGCGTACTTCGCGTACCGCCCGCCCCAGAGGCCCGCCTGCCGCC
GGCGGCAGGCGGGCCTCTGGGGCGGGCGGTACGCGAAGTACGCCGCCAACCAGGGGGGCCTCGCCCAGCGCCTCTCAGAGATGGCCGGGACCCTCAAGCG[G/A]
CTCCCCGAGGAGCTCGAGGAGACGATCAAGTCATCCTCGAGGGACCTCGCCCGGGGGGCGGTGGAGCTCGTACTGGCAAGCTACCAGGCCAGGGACCCTG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.80% | 0.00% | 2.37% | 48.88% | NA |
| All Indica | 2759 | 54.00% | 0.00% | 1.99% | 44.04% | NA |
| All Japonica | 1512 | 38.60% | 0.00% | 3.51% | 57.87% | NA |
| Aus | 269 | 53.50% | 0.00% | 0.37% | 46.10% | NA |
| Indica I | 595 | 32.80% | 0.00% | 3.87% | 63.36% | NA |
| Indica II | 465 | 36.80% | 0.00% | 2.15% | 61.08% | NA |
| Indica III | 913 | 78.50% | 0.00% | 1.10% | 20.37% | NA |
| Indica Intermediate | 786 | 51.70% | 0.00% | 1.53% | 46.82% | NA |
| Temperate Japonica | 767 | 28.60% | 0.00% | 5.22% | 66.23% | NA |
| Tropical Japonica | 504 | 51.80% | 0.00% | 1.59% | 46.63% | NA |
| Japonica Intermediate | 241 | 43.20% | 0.00% | 2.07% | 54.77% | NA |
| VI/Aromatic | 96 | 51.00% | 0.00% | 0.00% | 48.96% | NA |
| Intermediate | 90 | 42.20% | 0.00% | 3.33% | 54.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599207 | C -> T | LOC_Os08g19400.1 | synonymous_variant ; p.Arg232Arg; LOW | N | Average:21.523; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| vg0811599207 | C -> T | LOC_Os08g19380.1 | upstream_gene_variant ; 3284.0bp to feature; MODIFIER | N | Average:21.523; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| vg0811599207 | C -> T | LOC_Os08g19410.1 | upstream_gene_variant ; 4026.0bp to feature; MODIFIER | N | Average:21.523; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |
| vg0811599207 | C -> T | LOC_Os08g19390.1 | downstream_gene_variant ; 932.0bp to feature; MODIFIER | N | Average:21.523; most accessible tissue: Zhenshan97 flag leaf, score: 39.027 | N | N | N | N |