| Variant ID: vg0221509073 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509073 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTTGGCTGGACGACGTGGCCAACTTGGTCATGACGGCACGGCAGCGCCTAGGTGCTGGTGGGCGGTCCTCCGCCACCAAGACCTCTGGCGCTACTACCAC[C/T]
GGCTCCGTGTCGTCAAGGCGGAGGGCGCGGCGAGCGGCGGCTGTTGCTCGCCATTCGGCCGCCACTCCTTCGTCAGCGCCTCCGACCCAGGAAGATCTGC
GCAGATCTTCCTGGGTCGGAGGCGCTGACGAAGGAGTGGCGGCCGAATGGCGAGCAACAGCCGCCGCTCGCCGCGCCCTCCGCCTTGACGACACGGAGCC[G/A]
GTGGTAGTAGCGCCAGAGGTCTTGGTGGCGGAGGACCGCCCACCAGCACCTAGGCGCTGCCGTGCCGTCATGACCAAGTTGGCCACGTCGTCCAGCCAAC
| 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 | 35.30% | 0.20% | 0.49% | 64.01% | NA |
| All Indica | 2759 | 2.40% | 0.40% | 0.62% | 96.59% | NA |
| All Japonica | 1512 | 96.50% | 0.00% | 0.00% | 3.51% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.00% | 98.51% | NA |
| Indica I | 595 | 2.00% | 0.00% | 0.34% | 97.65% | NA |
| Indica II | 465 | 2.40% | 1.50% | 0.43% | 95.70% | NA |
| Indica III | 913 | 1.90% | 0.10% | 0.88% | 97.15% | NA |
| Indica Intermediate | 786 | 3.40% | 0.30% | 0.64% | 95.67% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.00% | 6.94% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 90.60% | 0.00% | 1.04% | 8.33% | NA |
| Intermediate | 90 | 56.70% | 0.00% | 5.56% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509073 | C -> T | LOC_Os02g35800.1 | synonymous_variant ; p.Thr137Thr; LOW | synonymous_codon | Average:10.207; most accessible tissue: Callus, score: 25.55 | N | N | N | N |
| vg0221509073 | C -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:10.207; most accessible tissue: Callus, score: 25.55 | N | N | N | N |