| Variant ID: vg1219400445 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 19400445 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.07, others allele: 0.00, population size: 227. )
CCCTGATTTTTTAAAAAAAAAGTTTACAGGCCAACCTCATAATGTTACACGCGTGATTTTCTCTGCATCGGTTATTGTTTGACCATCCAATATGTACCAG[C/T]
CATGCGGGCAGCTGAGCCATTCGTATATATGGTTATTAATTTAAGTGTGTGCAAGGTGTTCCATTCTGATCGGCACCGCAGCATGACCGGCGCCATAGAA
TTCTATGGCGCCGGTCATGCTGCGGTGCCGATCAGAATGGAACACCTTGCACACACTTAAATTAATAACCATATATACGAATGGCTCAGCTGCCCGCATG[G/A]
CTGGTACATATTGGATGGTCAAACAATAACCGATGCAGAGAAAATCACGCGTGTAACATTATGAGGTTGGCCTGTAAACTTTTTTTTTAAAAAATCAGGG
| 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 | 64.80% | 35.10% | 0.13% | 0.00% | NA |
| All Indica | 2759 | 43.00% | 56.90% | 0.18% | 0.00% | NA |
| All Japonica | 1512 | 98.40% | 1.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 40.00% | 60.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 78.30% | 21.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 24.30% | 75.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 45.90% | 53.70% | 0.38% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 17.80% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1219400445 | C -> T | LOC_Os12g32160.1 | downstream_gene_variant ; 4743.0bp to feature; MODIFIER | silent_mutation | Average:36.468; most accessible tissue: Callus, score: 65.574 | N | N | N | N |
| vg1219400445 | C -> T | LOC_Os12g32150-LOC_Os12g32160 | intergenic_region ; MODIFIER | silent_mutation | Average:36.468; most accessible tissue: Callus, score: 65.574 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1219400445 | 4.20E-06 | NA | mr1458 | 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 |
| vg1219400445 | 1.25E-07 | NA | mr1458_2 | 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 |
| vg1219400445 | 5.68E-08 | NA | mr1458_2 | Ind_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 |