| Variant ID: vg0221508689 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21508689 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTAGGGGGCTCTGCGAGAGATCTTCTGAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCCGAACAAGCAAAGGCGCACAA[C/T]
CTCTCTCCGAGCATTAGCGGTGACGATGGGGAGCCAAACCCATGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGAGGGAGGAGG
CCTCCTCCCTCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCATGGGTTTGGCTCCCCATCGTCACCGCTAATGCTCGGAGAGAG[G/A]
TTGTGCGCCTTTGCTTGTTCGGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTCAGAAGATCTCTCGCAGAGCCCCCTAC
| 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 | 36.00% | 0.30% | 0.44% | 63.25% | NA |
| All Indica | 2759 | 3.40% | 0.50% | 0.62% | 95.43% | NA |
| All Japonica | 1512 | 96.70% | 0.00% | 0.07% | 3.24% | NA |
| Aus | 269 | 0.70% | 0.00% | 0.00% | 99.26% | NA |
| Indica I | 595 | 3.90% | 0.00% | 0.34% | 95.80% | NA |
| Indica II | 465 | 3.00% | 2.20% | 0.22% | 94.62% | NA |
| Indica III | 913 | 3.20% | 0.10% | 0.88% | 95.84% | NA |
| Indica Intermediate | 786 | 3.70% | 0.40% | 0.76% | 95.17% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.13% | 1.30% | NA |
| Tropical Japonica | 504 | 93.50% | 0.00% | 0.00% | 6.55% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 3.33% | 35.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221508689 | C -> T | LOC_Os02g35800.1 | synonymous_variant ; p.Asn9Asn; LOW | synonymous_codon | Average:12.038; most accessible tissue: Callus, score: 31.066 | N | N | N | N |
| vg0221508689 | C -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:12.038; most accessible tissue: Callus, score: 31.066 | N | N | N | N |