| Variant ID: vg1223000007 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23000007 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGTAACATTATCCATATTCATATATATATTAATGAATCTTTTTTTAGATAATATATGTTAATAAATATAGACACACACATATATATATATACATATATAT[A/G]
TATATACATATATATATATATTATATATATATATATATAATATATATATATATATGTATGTGTGTGTTTAGATTTATTAACATCTATATAAATGTGAGCA
TGCTCACATTTATATAGATGTTAATAAATCTAAACACACACATACATATATATATATATATTATATATATATATATATAATATATATATATATGTATATA[T/C]
ATATATATGTATATATATATATGTGTGTGTCTATATTTATTAACATATATTATCTAAAAAAAGATTCATTAATATATATATGAATATGGATAATGTTACA
| 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 | 0.90% | 0.10% | 14.62% | 84.30% | NA |
| All Indica | 2759 | 0.60% | 0.30% | 9.79% | 89.34% | NA |
| All Japonica | 1512 | 1.20% | 0.00% | 20.17% | 78.64% | NA |
| Aus | 269 | 1.90% | 0.00% | 28.62% | 69.52% | NA |
| Indica I | 595 | 0.30% | 0.00% | 4.87% | 94.79% | NA |
| Indica II | 465 | 0.40% | 0.00% | 11.18% | 88.39% | NA |
| Indica III | 913 | 0.80% | 0.30% | 12.92% | 85.98% | NA |
| Indica Intermediate | 786 | 0.80% | 0.50% | 9.03% | 89.69% | NA |
| Temperate Japonica | 767 | 0.50% | 0.00% | 19.56% | 79.92% | NA |
| Tropical Japonica | 504 | 2.20% | 0.00% | 18.65% | 79.17% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 25.31% | 73.44% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 25.00% | 73.96% | NA |
| Intermediate | 90 | 3.30% | 0.00% | 16.67% | 80.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223000007 | A -> DEL | N | N | silent_mutation | Average:45.086; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |
| vg1223000007 | A -> G | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 251.0bp to feature; MODIFIER | silent_mutation | Average:45.086; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |
| vg1223000007 | A -> G | LOC_Os12g37470.1 | upstream_gene_variant ; 1483.0bp to feature; MODIFIER | silent_mutation | Average:45.086; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |
| vg1223000007 | A -> G | LOC_Os12g37490.1 | downstream_gene_variant ; 2204.0bp to feature; MODIFIER | silent_mutation | Average:45.086; most accessible tissue: Zhenshan97 flower, score: 69.089 | N | N | N | N |