| Variant ID: vg0335284080 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35284080 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGTTCACTTTGATGCTATTTTCAACCTTACCAAATTTTGGTAAAGTTGTTAAAAAAGTGGCTACATTTAGTTTGCTGCCAAATTTTGCTAACTATATAA[G/T]
AAATCATGCCAAAATTTTGGCAAGTTGCCAAACTTTTAGTAACTATGCCAAAATTTTGGCAATGCCAAAATTTAGTAAGGTTTTTTTTTGCAACAAAGTG
CACTTTGTTGCAAAAAAAAACCTTACTAAATTTTGGCATTGCCAAAATTTTGGCATAGTTACTAAAAGTTTGGCAACTTGCCAAAATTTTGGCATGATTT[C/A]
TTATATAGTTAGCAAAATTTGGCAGCAAACTAAATGTAGCCACTTTTTTAACAACTTTACCAAAATTTGGTAAGGTTGAAAATAGCATCAAAGTGAACAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.40% | 3.20% | 1.42% | 0.00% | NA |
| All Indica | 2759 | 99.10% | 0.00% | 0.87% | 0.00% | NA |
| All Japonica | 1512 | 88.20% | 9.30% | 2.51% | 0.00% | NA |
| Aus | 269 | 98.90% | 0.00% | 1.12% | 0.00% | NA |
| Indica I | 595 | 96.10% | 0.00% | 3.87% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 97.10% | 1.20% | 1.69% | 0.00% | NA |
| Tropical Japonica | 504 | 73.40% | 23.40% | 3.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 90.50% | 5.80% | 3.73% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 4.20% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335284080 | G -> T | LOC_Os03g62280.1 | upstream_gene_variant ; 918.0bp to feature; MODIFIER | silent_mutation | Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0335284080 | G -> T | LOC_Os03g62280.2 | upstream_gene_variant ; 918.0bp to feature; MODIFIER | silent_mutation | Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0335284080 | G -> T | LOC_Os03g62290.1 | downstream_gene_variant ; 4550.0bp to feature; MODIFIER | silent_mutation | Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| vg0335284080 | G -> T | LOC_Os03g62270-LOC_Os03g62280 | intergenic_region ; MODIFIER | silent_mutation | Average:40.209; most accessible tissue: Minghui63 panicle, score: 62.157 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0335284080 | 2.32E-06 | 2.99E-08 | mr1422_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 |
| vg0335284080 | NA | 7.60E-06 | mr1873_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 |
| vg0335284080 | 4.69E-07 | NA | mr1916_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 |