| Variant ID: vg0121350170 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21350170 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )
AGGGGTTCTACTGCTGCGAGGCACAAGGTGCGTATAGTTGAAAAGAGTAAAAAGGTACACAACTGCAAAAATCAGCTCGGTCTACAACCGCTTAAAATTA[C/G]
GTTCCGTCCTTATATATAGATTCATTTGTTTCTACCTTATTTCTCCCTCTGTTTTTTCTCTATTTGACATTGAACTAACCAACATCAGAAGTTTGGAAAC
GTTTCCAAACTTCTGATGTTGGTTAGTTCAATGTCAAATAGAGAAAAAACAGAGGGAGAAATAAGGTAGAAACAAATGAATCTATATATAAGGACGGAAC[G/C]
TAATTTTAAGCGGTTGTAGACCGAGCTGATTTTTGCAGTTGTGTACCTTTTTACTCTTTTCAACTATACGCACCTTGTGCCTCGCAGCAGTAGAACCCCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0121350170 | C -> G | LOC_Os01g38120.1 | upstream_gene_variant ; 496.0bp to feature; MODIFIER | silent_mutation | Average:67.666; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |
| vg0121350170 | C -> G | LOC_Os01g38140.1 | upstream_gene_variant ; 4300.0bp to feature; MODIFIER | silent_mutation | Average:67.666; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |
| vg0121350170 | C -> G | LOC_Os01g38130.1 | intron_variant ; MODIFIER | silent_mutation | Average:67.666; most accessible tissue: Zhenshan97 root, score: 79.452 | N | N | N | N |