| Variant ID: vg1101692470 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1692470 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTCCACCTCGTGATGGAGCTCTGCGCCGGCGGCGAGCTCTTCGACCGCATCATCGCGCGGGGCCACTACACGGAGCGCGCCGCGGCGGCGCTCCTCCGCG[C/T]
CATCGTCGGGATCGTGCACACCTGCCACTCCATGGGGGTGATCCACCGGGACCTCAAGCCGGAGAACTTCCTGCTGCTGAGCAAGGGGGACGACGCGCCG
CGGCGCGTCGTCCCCCTTGCTCAGCAGCAGGAAGTTCTCCGGCTTGAGGTCCCGGTGGATCACCCCCATGGAGTGGCAGGTGTGCACGATCCCGACGATG[G/A]
CGCGGAGGAGCGCCGCCGCGGCGCGCTCCGTGTAGTGGCCCCGCGCGATGATGCGGTCGAAGAGCTCGCCGCCGGCGCAGAGCTCCATCACGAGGTGGAC
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.10% | 0.80% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1101692470 | C -> T | LOC_Os11g04170.1 | missense_variant ; p.Ala190Val; MODERATE | N | Average:64.902; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |
| vg1101692470 | C -> T | LOC_Os11g04150.1 | upstream_gene_variant ; 4371.0bp to feature; MODIFIER | N | Average:64.902; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |
| vg1101692470 | C -> T | LOC_Os11g04160.1 | downstream_gene_variant ; 1130.0bp to feature; MODIFIER | N | Average:64.902; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |
| vg1101692470 | C -> T | LOC_Os11g04174.1 | downstream_gene_variant ; 2002.0bp to feature; MODIFIER | N | Average:64.902; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |
| vg1101692470 | C -> T | LOC_Os11g04180.1 | downstream_gene_variant ; 3957.0bp to feature; MODIFIER | N | Average:64.902; most accessible tissue: Zhenshan97 panicle, score: 84.824 | N | N | N | N |