| Variant ID: vg1205417446 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5417446 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCGCGCGGCGGCCGAGCGGGGCGCCTACGGCGAGGCGGCAAGGATCCTCGACGCGAGGCGGGAGGCGCTGAGCAGGTCGGCGCCGGCGGCGTCCGGCGA[C/T]
GCCATGTGCGCGGCGCTGGTGGCGGAGCTGCGGGAGCTGAGCGAGCGCGTGGCGGACGAGCGGGAGTACGCGCAGACGGGGCGCGCGTGCGTGCTCGCCG
CGGCGAGCACGCACGCGCGCCCCGTCTGCGCGTACTCCCGCTCGTCCGCCACGCGCTCGCTCAGCTCCCGCAGCTCCGCCACCAGCGCCGCGCACATGGC[G/A]
TCGCCGGACGCCGCCGGCGCCGACCTGCTCAGCGCCTCCCGCCTCGCGTCGAGGATCCTTGCCGCCTCGCCGTAGGCGCCCCGCTCGGCCGCCGCGCGCG
| 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 | 36.90% | 0.40% | 0.55% | 62.12% | NA |
| All Indica | 2759 | 5.10% | 0.10% | 0.29% | 94.49% | NA |
| All Japonica | 1512 | 92.60% | 1.00% | 0.99% | 5.42% | NA |
| Aus | 269 | 20.40% | 0.00% | 0.37% | 79.18% | NA |
| Indica I | 595 | 5.40% | 0.20% | 0.50% | 93.95% | NA |
| Indica II | 465 | 4.90% | 0.00% | 0.65% | 94.41% | NA |
| Indica III | 913 | 3.20% | 0.10% | 0.00% | 96.71% | NA |
| Indica Intermediate | 786 | 7.40% | 0.00% | 0.25% | 92.37% | NA |
| Temperate Japonica | 767 | 93.70% | 1.20% | 1.30% | 3.78% | NA |
| Tropical Japonica | 504 | 94.20% | 0.40% | 0.40% | 4.96% | NA |
| Japonica Intermediate | 241 | 85.50% | 1.70% | 1.24% | 11.62% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 66.70% | 1.10% | 2.22% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205417446 | C -> DEL | LOC_Os12g10250.1 | N | frameshift_variant | Average:12.138; most accessible tissue: Callus, score: 47.055 | N | N | N | N |
| vg1205417446 | C -> T | LOC_Os12g10250.1 | synonymous_variant ; p.Asp454Asp; LOW | synonymous_codon | Average:12.138; most accessible tissue: Callus, score: 47.055 | N | N | N | N |