| Variant ID: vg0103256578 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 3256578 |
| Reference Allele: G | Alternative Allele: T,C |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCAGTTTCAATAGACTTCAAGGAAGCATACCAATACCAGTAACCACATCCAGTGAGATCGCATTGGACTACTCAAACAACCACTTCTCTTCAATAGTACC[G/T,C]
AACTTTGGCATATATCTTGAAAACGCCAGCTATATTAATTTCTCCAATAATAAACTAAGTGGCAATGTACCATCTTCGATTTGTAATGCAAGCAAAGCCA
TGGCTTTGCTTGCATTACAAATCGAAGATGGTACATTGCCACTTAGTTTATTATTGGAGAAATTAATATAGCTGGCGTTTTCAAGATATATGCCAAAGTT[C/A,G]
GGTACTATTGAAGAGAAGTGGTTGTTTGAGTAGTCCAATGCGATCTCACTGGATGTGGTTACTGGTATTGGTATGCTTCCTTGAAGTCTATTGAAACTGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 68.80% | 26.00% | 1.33% | 3.83% | NA |
| All Indica | 2759 | 92.50% | 4.90% | 0.83% | 1.70% | NA |
| All Japonica | 1512 | 39.90% | 49.30% | 2.12% | 8.66% | NA |
| Aus | 269 | 13.80% | 83.30% | 2.97% | 0.00% | NA |
| Indica I | 595 | 97.80% | 2.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 92.50% | 6.00% | 0.22% | 1.29% | NA |
| Indica III | 913 | 88.00% | 6.50% | 1.64% | 3.94% | NA |
| Indica Intermediate | 786 | 93.90% | 4.70% | 0.76% | 0.64% | NA |
| Temperate Japonica | 767 | 56.20% | 26.50% | 2.74% | 14.60% | NA |
| Tropical Japonica | 504 | 18.70% | 80.00% | 0.60% | 0.79% | NA |
| Japonica Intermediate | 241 | 32.80% | 57.70% | 3.32% | 6.22% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 55.60% | 41.10% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0103256578 | G -> T | LOC_Os01g06876.1 | upstream_gene_variant ; 244.0bp to feature; MODIFIER | silent_mutation | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> T | LOC_Os01g06882.1 | upstream_gene_variant ; 1366.0bp to feature; MODIFIER | silent_mutation | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> T | LOC_Os01g06890.1 | upstream_gene_variant ; 2860.0bp to feature; MODIFIER | silent_mutation | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> T | LOC_Os01g06870.1 | downstream_gene_variant ; 3854.0bp to feature; MODIFIER | silent_mutation | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> T | LOC_Os01g06870-LOC_Os01g06876 | intergenic_region ; MODIFIER | silent_mutation | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> DEL | N | N | silent_mutation | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> C | LOC_Os01g06876.1 | upstream_gene_variant ; 244.0bp to feature; MODIFIER | N | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> C | LOC_Os01g06882.1 | upstream_gene_variant ; 1366.0bp to feature; MODIFIER | N | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> C | LOC_Os01g06890.1 | upstream_gene_variant ; 2860.0bp to feature; MODIFIER | N | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> C | LOC_Os01g06870.1 | downstream_gene_variant ; 3854.0bp to feature; MODIFIER | N | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |
| vg0103256578 | G -> C | LOC_Os01g06870-LOC_Os01g06876 | intergenic_region ; MODIFIER | N | Average:33.429; most accessible tissue: Zhenshan97 flower, score: 72.289 | N | N | N | N |