| Variant ID: vg0811599918 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599918 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGGGGGGGGGCGCGACGGGATCTCGCTGAGGCAGAAGAAAAACCAAAAGACAAAAAGAAACGGGTGAGTGAAAACTCGCCTTGGGAGATGGGAGAATGAA[T/C]
ACGGCCGCGGTGGGCGCGGGGACGAACCTGCGGGGAGGTCGGCTAAACGACCACCTCGGGGGTGAGATGAGGTTCCCCCGGCATGGCACAATCCCCCCCA
TGGGGGGGATTGTGCCATGCCGGGGGAACCTCATCTCACCCCCGAGGTGGTCGTTTAGCCGACCTCCCCGCAGGTTCGTCCCCGCGCCCACCGCGGCCGT[A/G]
TTCATTCTCCCATCTCCCAAGGCGAGTTTTCACTCACCCGTTTCTTTTTGTCTTTTGGTTTTTCTTCTGCCTCAGCGAGATCCCGTCGCGCCCCCCCCCC
| 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 | 2.40% | 0.90% | 2.52% | 94.22% | NA |
| All Indica | 2759 | 0.20% | 1.50% | 3.77% | 94.56% | NA |
| All Japonica | 1512 | 6.90% | 0.00% | 0.13% | 92.92% | NA |
| Aus | 269 | 0.00% | 0.00% | 4.46% | 95.54% | NA |
| Indica I | 595 | 0.00% | 0.50% | 1.01% | 98.49% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.65% | 99.35% | NA |
| Indica III | 913 | 0.20% | 3.30% | 8.87% | 87.62% | NA |
| Indica Intermediate | 786 | 0.40% | 1.00% | 1.78% | 96.82% | NA |
| Temperate Japonica | 767 | 8.90% | 0.00% | 0.13% | 91.00% | NA |
| Tropical Japonica | 504 | 4.60% | 0.00% | 0.00% | 95.44% | NA |
| Japonica Intermediate | 241 | 5.80% | 0.00% | 0.41% | 93.78% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 2.20% | 1.10% | 1.11% | 95.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599918 | T -> C | LOC_Os08g19380.1 | upstream_gene_variant ; 3995.0bp to feature; MODIFIER | silent_mutation | Average:10.063; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599918 | T -> C | LOC_Os08g19410.1 | upstream_gene_variant ; 3315.0bp to feature; MODIFIER | silent_mutation | Average:10.063; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599918 | T -> C | LOC_Os08g19390.1 | downstream_gene_variant ; 1643.0bp to feature; MODIFIER | silent_mutation | Average:10.063; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599918 | T -> C | LOC_Os08g19400.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.063; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599918 | T -> DEL | N | N | silent_mutation | Average:10.063; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |