| Variant ID: vg1223000075 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 23000075 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGACACACACATATATATATATACATATATATATATATACATATATATATATATTATATATATATATATATAATATATATATATATATGTATGTGTGTGT[T/C]
TAGATTTATTAACATCTATATAAATGTGAGCAATACTAAAAATTCTTATAACCTGAAACGTAGGAAATAATAATTAAGGTGCCAAAGTCTAGGTTTTCTT
AAGAAAACCTAGACTTTGGCACCTTAATTATTATTTCCTACGTTTCAGGTTATAAGAATTTTTAGTATTGCTCACATTTATATAGATGTTAATAAATCTA[A/G]
ACACACACATACATATATATATATATATTATATATATATATATATAATATATATATATATGTATATATATATATATGTATATATATATATGTGTGTGTCT
| 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 | 95.90% | 2.70% | 1.46% | 0.00% | NA |
| All Indica | 2759 | 94.90% | 3.00% | 2.14% | 0.00% | NA |
| All Japonica | 1512 | 97.40% | 2.10% | 0.53% | 0.00% | NA |
| Aus | 269 | 95.90% | 3.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 94.60% | 2.70% | 2.69% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 95.40% | 2.80% | 1.75% | 0.00% | NA |
| Indica Intermediate | 786 | 91.70% | 5.00% | 3.31% | 0.00% | NA |
| Temperate Japonica | 767 | 97.90% | 1.20% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.60% | 5.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 1.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1223000075 | T -> C | LOC_Os12g37480.1 | 3_prime_UTR_variant ; 183.0bp to feature; MODIFIER | silent_mutation | Average:60.641; most accessible tissue: Zhenshan97 flower, score: 82.718 | N | N | N | N |
| vg1223000075 | T -> C | LOC_Os12g37470.1 | upstream_gene_variant ; 1551.0bp to feature; MODIFIER | silent_mutation | Average:60.641; most accessible tissue: Zhenshan97 flower, score: 82.718 | N | N | N | N |
| vg1223000075 | T -> C | LOC_Os12g37490.1 | downstream_gene_variant ; 2136.0bp to feature; MODIFIER | silent_mutation | Average:60.641; most accessible tissue: Zhenshan97 flower, score: 82.718 | N | N | N | N |