| Variant ID: vg0234270181 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 34270181 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 96. )
ATTGAAGCCAAAATAGCCTAATAAGTTAACTATTGAAATGGCCTACTTTCTTAAGCATGCCAAAATTTGGTTTCAAACCAAAGGTCTGTTTACTTTGATG[C/T]
CATTTTCAACCTTACCAAATTTTGGTAACGTTGCTAAAAAAAAGTAGATACATTTAGTTTGCTGCCAAATTTTAGTAACTATATAAGAAATCCTGACAAA
TTTGTCAGGATTTCTTATATAGTTACTAAAATTTGGCAGCAAACTAAATGTATCTACTTTTTTTTAGCAACGTTACCAAAATTTGGTAAGGTTGAAAATG[G/A]
CATCAAAGTAAACAGACCTTTGGTTTGAAACCAAATTTTGGCATGCTTAAGAAAGTAGGCCATTTCAATAGTTAACTTATTAGGCTATTTTGGCTTCAAT
| 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 | 53.90% | 42.70% | 1.29% | 2.07% | NA |
| All Indica | 2759 | 29.50% | 66.30% | 0.83% | 3.41% | NA |
| All Japonica | 1512 | 92.30% | 5.60% | 1.92% | 0.13% | NA |
| Aus | 269 | 75.50% | 23.00% | 0.74% | 0.74% | NA |
| Indica I | 595 | 36.50% | 60.50% | 0.84% | 2.18% | NA |
| Indica II | 465 | 20.60% | 75.10% | 0.65% | 3.66% | NA |
| Indica III | 913 | 23.30% | 70.60% | 1.10% | 4.93% | NA |
| Indica Intermediate | 786 | 36.60% | 60.30% | 0.64% | 2.42% | NA |
| Temperate Japonica | 767 | 94.90% | 3.00% | 1.83% | 0.26% | NA |
| Tropical Japonica | 504 | 97.40% | 2.00% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 73.40% | 21.60% | 4.98% | 0.00% | NA |
| VI/Aromatic | 96 | 89.60% | 8.30% | 2.08% | 0.00% | NA |
| Intermediate | 90 | 53.30% | 41.10% | 5.56% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0234270181 | C -> T | LOC_Os02g56000.1 | upstream_gene_variant ; 246.0bp to feature; MODIFIER | silent_mutation | Average:62.452; most accessible tissue: Minghui63 flower, score: 80.659 | N | N | N | N |
| vg0234270181 | C -> T | LOC_Os02g56010.1 | upstream_gene_variant ; 4220.0bp to feature; MODIFIER | silent_mutation | Average:62.452; most accessible tissue: Minghui63 flower, score: 80.659 | N | N | N | N |
| vg0234270181 | C -> T | LOC_Os02g56000.2 | upstream_gene_variant ; 254.0bp to feature; MODIFIER | silent_mutation | Average:62.452; most accessible tissue: Minghui63 flower, score: 80.659 | N | N | N | N |
| vg0234270181 | C -> T | LOC_Os02g55990.1 | downstream_gene_variant ; 4365.0bp to feature; MODIFIER | silent_mutation | Average:62.452; most accessible tissue: Minghui63 flower, score: 80.659 | N | N | N | N |
| vg0234270181 | C -> T | LOC_Os02g56000-LOC_Os02g56010 | intergenic_region ; MODIFIER | silent_mutation | Average:62.452; most accessible tissue: Minghui63 flower, score: 80.659 | N | N | N | N |
| vg0234270181 | C -> DEL | N | N | silent_mutation | Average:62.452; most accessible tissue: Minghui63 flower, score: 80.659 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0234270181 | NA | 3.35E-08 | mr1925 | 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 |
| vg0234270181 | NA | 7.62E-06 | mr1091_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 |
| vg0234270181 | 1.06E-07 | 1.06E-07 | mr1973_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 |