| Variant ID: vg0137499770 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37499770 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCGATGTTGGCGCGGCCCCCTCCGGGCGCCTGTTACTGGCACGCGCCGCCCCGCCCCCTCGGGGAGGAGATGGGGGAAGTGTTCCTCCCTGCTTCCTCTT[C/T]
CCCCGGGCGTTGGCAGGGCGGCTGCTCCCCGGGCCCCTGTCGCGGGACCCAGAAGCACGACCCCCTCTCGGGGTAGATTGTTCCCCCCTGCGGCTCCCGC
GCGGGAGCCGCAGGGGGGAACAATCTACCCCGAGAGGGGGTCGTGCTTCTGGGTCCCGCGACAGGGGCCCGGGGAGCAGCCGCCCTGCCAACGCCCGGGG[G/A]
AAGAGGAAGCAGGGAGGAACACTTCCCCCATCTCCTCCCCGAGGGGGCGGGGCGGCGCGTGCCAGTAACAGGCGCCCGGAGGGGGCCGCGCCAACATCGC
| 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 | 35.90% | 0.30% | 0.57% | 63.27% | NA |
| All Indica | 2759 | 2.60% | 0.00% | 0.65% | 96.70% | NA |
| All Japonica | 1512 | 97.10% | 0.90% | 0.13% | 1.92% | NA |
| Aus | 269 | 1.10% | 0.00% | 2.23% | 96.65% | NA |
| Indica I | 595 | 1.80% | 0.00% | 0.50% | 97.65% | NA |
| Indica II | 465 | 1.50% | 0.00% | 0.65% | 97.85% | NA |
| Indica III | 913 | 1.40% | 0.00% | 0.66% | 97.92% | NA |
| Indica Intermediate | 786 | 5.30% | 0.00% | 0.76% | 93.89% | NA |
| Temperate Japonica | 767 | 98.40% | 0.00% | 0.00% | 1.56% | NA |
| Tropical Japonica | 504 | 94.80% | 2.40% | 0.40% | 2.38% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.40% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 1.11% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137499770 | C -> T | LOC_Os01g64610.1 | synonymous_variant ; p.Gly316Gly; LOW | synonymous_codon | Average:6.035; most accessible tissue: Callus, score: 17.235 | N | N | N | N |
| vg0137499770 | C -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:6.035; most accessible tissue: Callus, score: 17.235 | N | N | N | N |