| Variant ID: vg0209796881 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9796881 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 281. )
GTTTCTTGTATCAACAGATGGCTGACCGCGATGAGGAACAGATATTGTACGATACAATCGCGGAGGGAAGCAGCCAGTACTGGAATGAAGAAGAGGGGAA[C/T]
GAGGATCCAAACCAGTACTTGAACGAGGAAGGGAACGTGGAGAGGGATGCGGAGGGGAACCAGCAGGGGCACGTGGAAAGGGATGTGGAGGGGAACCAGG
CCTGGTTCCCCTCCACATCCCTTTCCACGTGCCCCTGCTGGTTCCCCTCCGCATCCCTCTCCACGTTCCCTTCCTCGTTCAAGTACTGGTTTGGATCCTC[G/A]
TTCCCCTCTTCTTCATTCCAGTACTGGCTGCTTCCCTCCGCGATTGTATCGTACAATATCTGTTCCTCATCGCGGTCAGCCATCTGTTGATACAAGAAAC
| 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 | 66.60% | 0.30% | 1.69% | 31.40% | NA |
| All Indica | 2759 | 50.80% | 0.50% | 2.79% | 45.92% | NA |
| All Japonica | 1512 | 98.90% | 0.00% | 0.07% | 0.99% | NA |
| Aus | 269 | 37.50% | 0.00% | 0.00% | 62.45% | NA |
| Indica I | 595 | 56.60% | 0.00% | 2.52% | 40.84% | NA |
| Indica II | 465 | 48.20% | 0.00% | 3.66% | 48.17% | NA |
| Indica III | 913 | 51.50% | 0.50% | 1.75% | 46.22% | NA |
| Indica Intermediate | 786 | 47.10% | 1.10% | 3.69% | 48.09% | NA |
| Temperate Japonica | 767 | 98.80% | 0.00% | 0.00% | 1.17% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 87.50% | 0.00% | 0.00% | 12.50% | NA |
| Intermediate | 90 | 73.30% | 0.00% | 2.22% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209796881 | C -> T | LOC_Os02g17110.1 | synonymous_variant ; p.Asn28Asn; LOW | synonymous_codon | Average:5.973; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |
| vg0209796881 | C -> DEL | LOC_Os02g17110.1 | N | frameshift_variant | Average:5.973; most accessible tissue: Zhenshan97 flower, score: 12.818 | N | N | N | N |