| Variant ID: vg0518766176 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 18766176 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 126. )
TCTTCCCCACGCCGCCGTTGCTGCTGCTGCTCCGAGGCCTCTTTTTCTCCGCCGTCGCCATTATCGCAGCGCTTGCTGGCTCCGTCTCGGAATCTTGATC[G/T]
GGTCTCTCTCCTCTCTCCTCTCTCACCCTATAAAAATATATGTTTGGCTTCTCACTATTACATAAAAAAAACATGAAGTTTGACATGATCAGTAAGCAAT
ATTGCTTACTGATCATGTCAAACTTCATGTTTTTTTTATGTAATAGTGAGAAGCCAAACATATATTTTTATAGGGTGAGAGAGGAGAGAGGAGAGAGACC[C/A]
GATCAAGATTCCGAGACGGAGCCAGCAAGCGCTGCGATAATGGCGACGGCGGAGAAAAAGAGGCCTCGGAGCAGCAGCAGCAACGGCGGCGTGGGGAAGA
| 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 | 91.70% | 4.50% | 3.77% | 0.00% | NA |
| All Indica | 2759 | 86.80% | 7.00% | 6.20% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 1.10% | 0.20% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
| Indica I | 595 | 90.40% | 1.20% | 8.40% | 0.00% | NA |
| Indica II | 465 | 72.90% | 20.40% | 6.67% | 0.00% | NA |
| Indica III | 913 | 98.80% | 0.50% | 0.66% | 0.00% | NA |
| Indica Intermediate | 786 | 78.40% | 10.90% | 10.69% | 0.00% | NA |
| Temperate Japonica | 767 | 97.80% | 1.80% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 5.60% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0518766176 | G -> T | LOC_Os05g32180.1 | 5_prime_UTR_variant ; 40.0bp to feature; MODIFIER | silent_mutation | Average:60.069; most accessible tissue: Callus, score: 79.004 | N | N | N | N |
| vg0518766176 | G -> T | LOC_Os05g32190.1 | downstream_gene_variant ; 2864.0bp to feature; MODIFIER | silent_mutation | Average:60.069; most accessible tissue: Callus, score: 79.004 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0518766176 | 3.41E-07 | 3.41E-07 | mr1956_2 | 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 |
| vg0518766176 | NA | 1.64E-06 | mr1956_2 | Ind_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 |