| Variant ID: vg1204614277 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 4614277 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGAAAATACAAAGGAGAAGTGGGAAAAAATCCAGAAGGATTGATGGGGCTTAAAAGAATTTTACTAAGGAGTGAAATATCATGTATATATCAATGGAGCC[C/T]
GGTTAAACTGTAATTTTTATCAACAAATATATTATTTCCAACATATATACTTATATTAAATCCTTTAGCTCATAAAAACATTTTATACATTTGCAAACAA
TTGTTTGCAAATGTATAAAATGTTTTTATGAGCTAAAGGATTTAATATAAGTATATATGTTGGAAATAATATATTTGTTGATAAAAATTACAGTTTAACC[G/A]
GGCTCCATTGATATATACATGATATTTCACTCCTTAGTAAAATTCTTTTAAGCCCCATCAATCCTTCTGGATTTTTTCCCACTTCTCCTTTGTATTTTCT
| 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 | 97.90% | 1.10% | 1.02% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 93.70% | 3.40% | 2.91% | 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 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 87.90% | 6.60% | 5.48% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1204614277 | C -> T | LOC_Os12g08890.1 | downstream_gene_variant ; 1956.0bp to feature; MODIFIER | silent_mutation | Average:35.177; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| vg1204614277 | C -> T | LOC_Os12g08880-LOC_Os12g08890 | intergenic_region ; MODIFIER | silent_mutation | Average:35.177; most accessible tissue: Zhenshan97 panicle, score: 49.416 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1204614277 | 6.95E-06 | 6.95E-06 | mr1915 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1204614277 | 1.14E-06 | 1.14E-06 | mr1081_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1204614277 | NA | 9.42E-06 | mr1204_2 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |