| Variant ID: vg1223000091 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23000091 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATATATACATATATATATATATACATATATATATATATTATATATATATATATATAATATATATATATATATGTATGTGTGTGTTTAGATTTATTAACAT[C/T]
TATATAAATGTGAGCAATACTAAAAATTCTTATAACCTGAAACGTAGGAAATAATAATTAAGGTGCCAAAGTCTAGGTTTTCTTTCTATCGCTATATATA
TATATATAGCGATAGAAAGAAAACCTAGACTTTGGCACCTTAATTATTATTTCCTACGTTTCAGGTTATAAGAATTTTTAGTATTGCTCACATTTATATA[G/A]
ATGTTAATAAATCTAAACACACACATACATATATATATATATATTATATATATATATATATAATATATATATATATGTATATATATATATATGTATATAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 43.40% | 6.40% | 10.69% | 39.50% | NA |
| All Indica | 2759 | 14.10% | 7.50% | 13.05% | 65.35% | NA |
| All Japonica | 1512 | 93.70% | 4.80% | 0.20% | 1.32% | NA |
| Aus | 269 | 35.70% | 6.30% | 48.33% | 9.67% | NA |
| Indica I | 595 | 47.10% | 7.10% | 1.51% | 44.37% | NA |
| Indica II | 465 | 6.90% | 3.70% | 25.59% | 63.87% | NA |
| Indica III | 913 | 2.80% | 6.80% | 12.27% | 78.09% | NA |
| Indica Intermediate | 786 | 6.50% | 10.90% | 15.27% | 67.30% | NA |
| Temperate Japonica | 767 | 94.10% | 3.90% | 0.26% | 1.69% | NA |
| Tropical Japonica | 504 | 96.00% | 2.60% | 0.20% | 1.19% | NA |
| Japonica Intermediate | 241 | 87.60% | 12.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 88.50% | 2.10% | 6.25% | 3.12% | NA |
| Intermediate | 90 | 70.00% | 6.70% | 6.67% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223000091 | C -> DEL | N | N | silent_mutation | Average:60.093; most accessible tissue: Zhenshan97 flower, score: 83.283 | N | N | N | N |
| vg1223000091 | C -> T | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 167.0bp to feature; MODIFIER | silent_mutation | Average:60.093; most accessible tissue: Zhenshan97 flower, score: 83.283 | N | N | N | N |
| vg1223000091 | C -> T | LOC_Os12g37470.1 | upstream_gene_variant ; 1567.0bp to feature; MODIFIER | silent_mutation | Average:60.093; most accessible tissue: Zhenshan97 flower, score: 83.283 | N | N | N | N |
| vg1223000091 | C -> T | LOC_Os12g37490.1 | downstream_gene_variant ; 2120.0bp to feature; MODIFIER | silent_mutation | Average:60.093; most accessible tissue: Zhenshan97 flower, score: 83.283 | N | N | N | N |