| Variant ID: vg0811599869 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11599869 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTCTCCTCGGCCACAGACCGGCCGGACTTGGAATGGCGGGGGGGGGGAAGGGGGGGGGGCGCGACGGGATCTCGCTGAGGCAGAAGAAAAACCAAAAGAC[A/G]
AAAAGAAACGGGTGAGTGAAAACTCGCCTTGGGAGATGGGAGAATGAATACGGCCGCGGTGGGCGCGGGGACGAACCTGCGGGGAGGTCGGCTAAACGAC
GTCGTTTAGCCGACCTCCCCGCAGGTTCGTCCCCGCGCCCACCGCGGCCGTATTCATTCTCCCATCTCCCAAGGCGAGTTTTCACTCACCCGTTTCTTTT[T/C]
GTCTTTTGGTTTTTCTTCTGCCTCAGCGAGATCCCGTCGCGCCCCCCCCCCTTCCCCCCCCCCGCCATTCCAAGTCCGGCCGGTCTGTGGCCGAGGAGAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 2.40% | 0.20% | 2.52% | 94.92% | NA |
| All Indica | 2759 | 0.20% | 0.30% | 3.81% | 95.69% | NA |
| All Japonica | 1512 | 6.90% | 0.00% | 0.26% | 92.79% | NA |
| Aus | 269 | 0.00% | 0.00% | 3.72% | 96.28% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.34% | 99.66% | NA |
| Indica II | 465 | 0.00% | 0.00% | 0.43% | 99.57% | NA |
| Indica III | 913 | 0.30% | 0.40% | 8.87% | 90.36% | NA |
| Indica Intermediate | 786 | 0.40% | 0.50% | 2.54% | 96.56% | NA |
| Temperate Japonica | 767 | 8.90% | 0.00% | 0.39% | 90.74% | 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% | 0.00% | 0.00% | 97.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811599869 | A -> G | LOC_Os08g19380.1 | upstream_gene_variant ; 3946.0bp to feature; MODIFIER | silent_mutation | Average:10.848; most accessible tissue: Zhenshan97 young leaf, score: 18.248 | N | N | N | N |
| vg0811599869 | A -> G | LOC_Os08g19410.1 | upstream_gene_variant ; 3364.0bp to feature; MODIFIER | silent_mutation | Average:10.848; most accessible tissue: Zhenshan97 young leaf, score: 18.248 | N | N | N | N |
| vg0811599869 | A -> G | LOC_Os08g19390.1 | downstream_gene_variant ; 1594.0bp to feature; MODIFIER | silent_mutation | Average:10.848; most accessible tissue: Zhenshan97 young leaf, score: 18.248 | N | N | N | N |
| vg0811599869 | A -> G | LOC_Os08g19400.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.848; most accessible tissue: Zhenshan97 young leaf, score: 18.248 | N | N | N | N |
| vg0811599869 | A -> DEL | N | N | silent_mutation | Average:10.848; most accessible tissue: Zhenshan97 young leaf, score: 18.248 | N | N | N | N |