| Variant ID: vg0234179772 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34179772 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )
TTTTAACCGATGCAGACCATCAGTGGAATGCCACTTATTTTATTTTAAAGGTTGTATTACCTTACAAGGATTTACTTACTGTTTTCCTTCAAACACGTAA[T/C]
GGCCCAAAAAACAGTGACGGCCAGCCAATACTGACTGATCATACCTGGCACATTGTTGAAAGGTTCAATCAATTTCTTGAAACGTTTCATGACTGTACTC
GAGTACAGTCATGAAACGTTTCAAGAAATTGATTGAACCTTTCAACAATGTGCCAGGTATGATCAGTCAGTATTGGCTGGCCGTCACTGTTTTTTGGGCC[A/G]
TTACGTGTTTGAAGGAAAACAGTAAGTAAATCCTTGTAAGGTAATACAACCTTTAAAATAAAATAAGTGGCATTCCACTGATGGTCTGCATCGGTTAAAA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.60% | 0.20% | 6.83% | 39.34% | NA |
| All Indica | 2759 | 31.10% | 0.10% | 8.08% | 60.75% | NA |
| All Japonica | 1512 | 97.80% | 0.00% | 0.13% | 2.05% | NA |
| Aus | 269 | 37.90% | 3.00% | 29.00% | 30.11% | NA |
| Indica I | 595 | 23.20% | 0.00% | 4.37% | 72.44% | NA |
| Indica II | 465 | 23.90% | 0.00% | 3.66% | 72.47% | NA |
| Indica III | 913 | 37.90% | 0.10% | 14.57% | 47.43% | NA |
| Indica Intermediate | 786 | 33.50% | 0.10% | 5.98% | 60.43% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.13% | 2.09% | NA |
| Tropical Japonica | 504 | 99.40% | 0.00% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 94.60% | 0.00% | 0.41% | 4.98% | NA |
| VI/Aromatic | 96 | 36.50% | 1.00% | 13.54% | 48.96% | NA |
| Intermediate | 90 | 65.60% | 0.00% | 7.78% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234179772 | T -> DEL | N | N | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179772 | T -> C | LOC_Os02g55840.1 | upstream_gene_variant ; 2313.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179772 | T -> C | LOC_Os02g55840.2 | upstream_gene_variant ; 2313.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179772 | T -> C | LOC_Os02g55840.5 | upstream_gene_variant ; 2313.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179772 | T -> C | LOC_Os02g55840.4 | upstream_gene_variant ; 2313.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179772 | T -> C | LOC_Os02g55840.3 | upstream_gene_variant ; 2313.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179772 | T -> C | LOC_Os02g55840.6 | upstream_gene_variant ; 2315.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179772 | T -> C | LOC_Os02g55830.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |