| Variant ID: vg0121350176 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 21350176 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 232. )
TCTACTGCTGCGAGGCACAAGGTGCGTATAGTTGAAAAGAGTAAAAAGGTACACAACTGCAAAAATCAGCTCGGTCTACAACCGCTTAAAATTACGTTCC[G/A]
TCCTTATATATAGATTCATTTGTTTCTACCTTATTTCTCCCTCTGTTTTTTCTCTATTTGACATTGAACTAACCAACATCAGAAGTTTGGAAACATAGAC
GTCTATGTTTCCAAACTTCTGATGTTGGTTAGTTCAATGTCAAATAGAGAAAAAACAGAGGGAGAAATAAGGTAGAAACAAATGAATCTATATATAAGGA[C/T]
GGAACGTAATTTTAAGCGGTTGTAGACCGAGCTGATTTTTGCAGTTGTGTACCTTTTTACTCTTTTCAACTATACGCACCTTGTGCCTCGCAGCAGTAGA
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 68.00% | 32.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.20% | 5.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0121350176 | G -> A | LOC_Os01g38120.1 | upstream_gene_variant ; 502.0bp to feature; MODIFIER | silent_mutation | Average:70.396; most accessible tissue: Callus, score: 80.173 | N | N | N | N |
| vg0121350176 | G -> A | LOC_Os01g38140.1 | upstream_gene_variant ; 4294.0bp to feature; MODIFIER | silent_mutation | Average:70.396; most accessible tissue: Callus, score: 80.173 | N | N | N | N |
| vg0121350176 | G -> A | LOC_Os01g38130.1 | intron_variant ; MODIFIER | silent_mutation | Average:70.396; most accessible tissue: Callus, score: 80.173 | N | N | N | N |