| Variant ID: vg0324794198 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr03 | Position: 24794198 |
| Reference Allele: CA | Alternative Allele: C |
| Primary Allele: CA | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CCTGTGATAGAGGTTGCTGGGCTCGTCGATCGGACAAATTGCGTTGATTTGTCATGGTCATCTGAGAAGAGCCTTTCGATGGCATTGCTTTCCTAACCCC[CA/C]
AAAAAAAGAAAGAAAAAAGAAATACACAATCCTTATCAGAGAGGGATTTACACCTACAGTGCCAATGAAACAAACTAGTTCCAAGTAGTCAGCTTAAAAA
TTTTTAAGCTGACTACTTGGAACTAGTTTGTTTCATTGGCACTGTAGGTGTAAATCCCTCTCTGATAAGGATTGTGTATTTCTTTTTTCTTTCTTTTTTT[TG/G]
GGGGTTAGGAAAGCAATGCCATCGAAAGGCTCTTCTCAGATGACCATGACAAATCAACGCAATTTGTCCGATCGACGAGCCCAGCAACCTCTATCACAGG
| Populations | Population Size | Frequency of CA(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.80% | 0.30% | 6.18% | 26.68% | NA |
| All Indica | 2759 | 49.70% | 0.10% | 7.54% | 42.66% | NA |
| All Japonica | 1512 | 99.10% | 0.30% | 0.13% | 0.46% | NA |
| Aus | 269 | 49.10% | 3.00% | 27.51% | 20.45% | NA |
| Indica I | 595 | 78.20% | 0.00% | 5.38% | 16.47% | NA |
| Indica II | 465 | 22.80% | 0.00% | 4.95% | 72.26% | NA |
| Indica III | 913 | 39.00% | 0.10% | 12.05% | 48.85% | NA |
| Indica Intermediate | 786 | 56.50% | 0.30% | 5.47% | 37.79% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.13% | 0.39% | NA |
| Tropical Japonica | 504 | 98.40% | 0.80% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.40% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 93.80% | 0.00% | 3.12% | 3.12% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 5.56% | 21.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0324794198 | CA -> C | LOC_Os03g44140.1 | downstream_gene_variant ; 3605.0bp to feature; MODIFIER | silent_mutation | Average:11.241; most accessible tissue: Zhenshan97 flower, score: 32.793 | N | N | N | N |
| vg0324794198 | CA -> C | LOC_Os03g44130.1 | intron_variant ; MODIFIER | silent_mutation | Average:11.241; most accessible tissue: Zhenshan97 flower, score: 32.793 | N | N | N | N |
| vg0324794198 | CA -> DEL | N | N | silent_mutation | Average:11.241; most accessible tissue: Zhenshan97 flower, score: 32.793 | N | N | N | N |