| Variant ID: vg0234179822 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34179822 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GTTGTATTACCTTACAAGGATTTACTTACTGTTTTCCTTCAAACACGTAATGGCCCAAAAAACAGTGACGGCCAGCCAATACTGACTGATCATACCTGGC[A/G]
CATTGTTGAAAGGTTCAATCAATTTCTTGAAACGTTTCATGACTGTACTCTTCTGTTATCTCAAGTATATTATCCAACAGCTAATTTAATTTTGCATAAT
ATTATGCAAAATTAAATTAGCTGTTGGATAATATACTTGAGATAACAGAAGAGTACAGTCATGAAACGTTTCAAGAAATTGATTGAACCTTTCAACAATG[T/C]
GCCAGGTATGATCAGTCAGTATTGGCTGGCCGTCACTGTTTTTTGGGCCATTACGTGTTTGAAGGAAAACAGTAAGTAAATCCTTGTAAGGTAATACAAC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.40% | 11.70% | 6.88% | 35.97% | NA |
| All Indica | 2759 | 18.80% | 18.10% | 8.92% | 54.19% | NA |
| All Japonica | 1512 | 94.40% | 3.20% | 0.33% | 2.05% | NA |
| Aus | 269 | 41.60% | 0.00% | 21.19% | 37.17% | NA |
| Indica I | 595 | 9.20% | 16.00% | 4.37% | 70.42% | NA |
| Indica II | 465 | 24.90% | 8.40% | 6.24% | 60.43% | NA |
| Indica III | 913 | 21.20% | 24.80% | 14.13% | 39.87% | NA |
| Indica Intermediate | 786 | 19.70% | 17.60% | 7.89% | 54.83% | NA |
| Temperate Japonica | 767 | 97.70% | 0.00% | 0.39% | 1.96% | NA |
| Tropical Japonica | 504 | 89.90% | 9.30% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.40% | 0.83% | 4.98% | NA |
| VI/Aromatic | 96 | 36.50% | 1.00% | 11.46% | 51.04% | NA |
| Intermediate | 90 | 57.80% | 7.80% | 6.67% | 27.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234179822 | A -> G | LOC_Os02g55840.1 | upstream_gene_variant ; 2263.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179822 | A -> G | LOC_Os02g55840.2 | upstream_gene_variant ; 2263.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179822 | A -> G | LOC_Os02g55840.5 | upstream_gene_variant ; 2263.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179822 | A -> G | LOC_Os02g55840.4 | upstream_gene_variant ; 2263.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179822 | A -> G | LOC_Os02g55840.3 | upstream_gene_variant ; 2263.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179822 | A -> G | LOC_Os02g55840.6 | upstream_gene_variant ; 2265.0bp to feature; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179822 | A -> G | LOC_Os02g55830.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |
| vg0234179822 | A -> DEL | N | N | silent_mutation | Average:4.975; most accessible tissue: Callus, score: 10.052 | N | N | N | N |