| Variant ID: vg0811599925 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599925 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGGCGCGACGGGATCTCGCTGAGGCAGAAGAAAAACCAAAAGACAAAAAGAAACGGGTGAGTGAAAACTCGCCTTGGGAGATGGGAGAATGAATACGGCC[G/A]
CGGTGGGCGCGGGGACGAACCTGCGGGGAGGTCGGCTAAACGACCACCTCGGGGGTGAGATGAGGTTCCCCCGGCATGGCACAATCCCCCCCATCTTGCG
CGCAAGATGGGGGGGATTGTGCCATGCCGGGGGAACCTCATCTCACCCCCGAGGTGGTCGTTTAGCCGACCTCCCCGCAGGTTCGTCCCCGCGCCCACCG[C/T]
GGCCGTATTCATTCTCCCATCTCCCAAGGCGAGTTTTCACTCACCCGTTTCTTTTTGTCTTTTGGTTTTTCTTCTGCCTCAGCGAGATCCCGTCGCGCCC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 5.00% | 0.30% | 3.17% | 91.52% | NA |
| All Indica | 2759 | 3.70% | 0.50% | 4.31% | 91.48% | NA |
| All Japonica | 1512 | 8.30% | 0.00% | 0.86% | 90.81% | NA |
| Aus | 269 | 1.90% | 0.00% | 5.20% | 92.94% | NA |
| Indica I | 595 | 2.40% | 0.00% | 2.35% | 95.29% | NA |
| Indica II | 465 | 0.20% | 0.00% | 0.65% | 99.14% | NA |
| Indica III | 913 | 7.60% | 1.20% | 8.32% | 82.91% | NA |
| Indica Intermediate | 786 | 2.40% | 0.30% | 3.31% | 94.02% | NA |
| Temperate Japonica | 767 | 11.00% | 0.00% | 0.26% | 88.79% | NA |
| Tropical Japonica | 504 | 5.40% | 0.00% | 1.39% | 93.25% | NA |
| Japonica Intermediate | 241 | 6.20% | 0.00% | 1.66% | 92.12% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 3.12% | 96.88% | NA |
| Intermediate | 90 | 3.30% | 1.10% | 1.11% | 94.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599925 | G -> A | LOC_Os08g19380.1 | upstream_gene_variant ; 4002.0bp to feature; MODIFIER | silent_mutation | Average:10.773; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599925 | G -> A | LOC_Os08g19410.1 | upstream_gene_variant ; 3308.0bp to feature; MODIFIER | silent_mutation | Average:10.773; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599925 | G -> A | LOC_Os08g19390.1 | downstream_gene_variant ; 1650.0bp to feature; MODIFIER | silent_mutation | Average:10.773; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599925 | G -> A | LOC_Os08g19400.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.773; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |
| vg0811599925 | G -> DEL | N | N | silent_mutation | Average:10.773; most accessible tissue: Zhenshan97 young leaf, score: 16.877 | N | N | N | N |