| Variant ID: vg1225600745 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 25600745 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGTTGTCTTAACGTCCATTTGATGAACGAGAAGACCATGTGAGGCTGCTAGGGAAAGTAGCACACGAATTGTGGTCAATCTAGCAACATGTGAGTAAGTG[T/C]
CAAAGAAATCTTCGCCTTCTTTCTGAGTATAGCCCTTAGCAACAAGCCGAGCCTTGTACTTTTCAATAGTACCGTCAGGCCTAAGCTTCTTCTTGAACAC
GTGTTCAAGAAGAAGCTTAGGCCTGACGGTACTATTGAAAAGTACAAGGCTCGGCTTGTTGCTAAGGGCTATACTCAGAAAGAAGGCGAAGATTTCTTTG[A/G]
CACTTACTCACATGTTGCTAGATTGACCACAATTCGTGTGCTACTTTCCCTAGCAGCCTCACATGGTCTTCTCGTTCATCAAATGGACGTTAAGACAACT
| 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 | 54.30% | 1.90% | 12.00% | 31.78% | NA |
| All Indica | 2759 | 43.10% | 0.30% | 12.79% | 43.86% | NA |
| All Japonica | 1512 | 82.70% | 5.10% | 12.04% | 0.13% | NA |
| Aus | 269 | 5.60% | 0.00% | 4.09% | 90.33% | NA |
| Indica I | 595 | 86.90% | 0.00% | 2.52% | 10.59% | NA |
| Indica II | 465 | 18.70% | 0.90% | 14.62% | 65.81% | NA |
| Indica III | 913 | 30.10% | 0.00% | 20.37% | 49.51% | NA |
| Indica Intermediate | 786 | 39.40% | 0.40% | 10.69% | 49.49% | NA |
| Temperate Japonica | 767 | 88.40% | 0.00% | 11.60% | 0.00% | NA |
| Tropical Japonica | 504 | 81.90% | 14.10% | 3.97% | 0.00% | NA |
| Japonica Intermediate | 241 | 66.40% | 2.50% | 30.29% | 0.83% | NA |
| VI/Aromatic | 96 | 60.40% | 0.00% | 13.54% | 26.04% | NA |
| Intermediate | 90 | 58.90% | 7.80% | 8.89% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1225600745 | T -> C | LOC_Os12g41280.1 | missense_variant ; p.Asp873Gly; MODERATE | nonsynonymous_codon ; D873G | Average:12.04; most accessible tissue: Zhenshan97 root, score: 25.639 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1225600745 | T -> DEL | LOC_Os12g41280.1 | N | frameshift_variant | Average:12.04; most accessible tissue: Zhenshan97 root, score: 25.639 | N | N | N | N |