| Variant ID: vg0234179816 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34179816 |
| 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: 354. )
TTAAAGGTTGTATTACCTTACAAGGATTTACTTACTGTTTTCCTTCAAACACGTAATGGCCCAAAAAACAGTGACGGCCAGCCAATACTGACTGATCATA[C/G]
CTGGCACATTGTTGAAAGGTTCAATCAATTTCTTGAAACGTTTCATGACTGTACTCTTCTGTTATCTCAAGTATATTATCCAACAGCTAATTTAATTTTG
CAAAATTAAATTAGCTGTTGGATAATATACTTGAGATAACAGAAGAGTACAGTCATGAAACGTTTCAAGAAATTGATTGAACCTTTCAACAATGTGCCAG[G/C]
TATGATCAGTCAGTATTGGCTGGCCGTCACTGTTTTTTGGGCCATTACGTGTTTGAAGGAAAACAGTAAGTAAATCCTTGTAAGGTAATACAACCTTTAA
| 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 | 57.70% | 0.10% | 6.35% | 35.84% | NA |
| All Indica | 2759 | 37.20% | 0.10% | 7.68% | 54.98% | NA |
| All Japonica | 1512 | 97.80% | 0.00% | 0.26% | 1.98% | NA |
| Aus | 269 | 44.20% | 1.10% | 24.16% | 30.48% | NA |
| Indica I | 595 | 27.10% | 0.00% | 2.52% | 70.42% | NA |
| Indica II | 465 | 32.30% | 0.20% | 4.09% | 63.44% | NA |
| Indica III | 913 | 45.80% | 0.10% | 13.80% | 40.31% | NA |
| Indica Intermediate | 786 | 37.90% | 0.10% | 6.62% | 55.34% | NA |
| Temperate Japonica | 767 | 97.50% | 0.00% | 0.52% | 1.96% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.00% | 0.00% | 4.98% | NA |
| VI/Aromatic | 96 | 39.60% | 0.00% | 15.62% | 44.79% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 4.44% | 24.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234179816 | C -> G | LOC_Os02g55840.1 | upstream_gene_variant ; 2269.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179816 | C -> G | LOC_Os02g55840.2 | upstream_gene_variant ; 2269.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179816 | C -> G | LOC_Os02g55840.5 | upstream_gene_variant ; 2269.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179816 | C -> G | LOC_Os02g55840.4 | upstream_gene_variant ; 2269.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179816 | C -> G | LOC_Os02g55840.3 | upstream_gene_variant ; 2269.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179816 | C -> G | LOC_Os02g55840.6 | upstream_gene_variant ; 2271.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179816 | C -> G | LOC_Os02g55830.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179816 | C -> DEL | N | N | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |