| Variant ID: vg0603482934 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 3482934 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTATCAATCTATATATTCCGGTGAATTACTTATTTATAAACACGATCATTATAGTGGTGATCATCATTTCATGTGTTCCTATATTTCATGTGGGATTGGA[T/C]
TCAAATGAATTGGATTTGATTTTACTGTTTCTTTTAGCTAATCATGGCATCAAGCTATCAACATGGTCCGAATATTTAATATTTGAACTATAAATTAAAT
ATTTAATTTATAGTTCAAATATTAAATATTCGGACCATGTTGATAGCTTGATGCCATGATTAGCTAAAAGAAACAGTAAAATCAAATCCAATTCATTTGA[A/G]
TCCAATCCCACATGAAATATAGGAACACATGAAATGATGATCACCACTATAATGATCGTGTTTATAAATAAGTAATTCACCGGAATATATAGATTGATAC
| 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 | 66.00% | 0.40% | 8.23% | 25.35% | NA |
| All Indica | 2759 | 75.50% | 0.00% | 3.81% | 20.70% | NA |
| All Japonica | 1512 | 40.70% | 1.30% | 18.06% | 39.95% | NA |
| Aus | 269 | 98.90% | 0.00% | 0.74% | 0.37% | NA |
| Indica I | 595 | 66.40% | 0.00% | 3.03% | 30.59% | NA |
| Indica II | 465 | 81.50% | 0.00% | 2.80% | 15.70% | NA |
| Indica III | 913 | 78.00% | 0.00% | 4.05% | 17.96% | NA |
| Indica Intermediate | 786 | 76.00% | 0.00% | 4.71% | 19.34% | NA |
| Temperate Japonica | 767 | 56.70% | 0.30% | 4.04% | 38.98% | NA |
| Tropical Japonica | 504 | 23.60% | 3.00% | 39.09% | 34.33% | NA |
| Japonica Intermediate | 241 | 25.70% | 0.80% | 18.67% | 54.77% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 7.29% | 1.04% | NA |
| Intermediate | 90 | 74.40% | 0.00% | 2.22% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0603482934 | T -> C | LOC_Os06g07270.1 | downstream_gene_variant ; 691.0bp to feature; MODIFIER | silent_mutation | Average:14.146; most accessible tissue: Callus, score: 41.206 | N | N | N | N |
| vg0603482934 | T -> C | LOC_Os06g07260-LOC_Os06g07270 | intergenic_region ; MODIFIER | silent_mutation | Average:14.146; most accessible tissue: Callus, score: 41.206 | N | N | N | N |
| vg0603482934 | T -> DEL | N | N | silent_mutation | Average:14.146; most accessible tissue: Callus, score: 41.206 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0603482934 | 1.49E-06 | NA | mr1392 | 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 |
| vg0603482934 | NA | 9.21E-08 | mr1408 | 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 |
| vg0603482934 | NA | 2.88E-06 | mr1682 | 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 |