| Variant ID: vg0333682687 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 33682687 |
| Reference Allele: C | Alternative Allele: T,A |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 108. )
TCCCATTTTATGGTCTACGGTGTCAGGGACCTCTTATACGGGTAAAAAGAAGAGAAAAAAACAAATCCATTATTCTCTTCTCTGAAATACTCCATCCGTT[C/T,A]
CCAAATATTTGACGCCGTTGATTTTTTTAAATATGTTTGACCATTCGTCTTATTAAAAAAAATAAGTAACTATTAATTTTTTTTCCTATTATTTGATTCA
TGAATCAAATAATAGGAAAAAAAATTAATAGTTACTTATTTTTTTTAATAAGACGAATGGTCAAACATATTTAAAAAAATCAACGGCGTCAAATATTTGG[G/A,T]
AACGGATGGAGTATTTCAGAGAAGAGAATAATGGATTTGTTTTTTTCTCTTCTTTTTACCCGTATAAGAGGTCCCTGACACCGTAGACCATAAAATGGGA
| 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 | 89.30% | 10.50% | 0.08% | 0.00% | A: 0.11% |
| All Indica | 2759 | 82.60% | 17.10% | 0.11% | 0.00% | A: 0.18% |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.50% | 1.10% | 0.37% | 0.00% | NA |
| Indica I | 595 | 95.10% | 4.70% | 0.17% | 0.00% | NA |
| Indica II | 465 | 82.60% | 17.20% | 0.00% | 0.00% | A: 0.22% |
| Indica III | 913 | 74.30% | 25.20% | 0.11% | 0.00% | A: 0.44% |
| Indica Intermediate | 786 | 82.70% | 17.20% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 81.10% | 18.90% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0333682687 | C -> T | LOC_Os03g59152.1 | upstream_gene_variant ; 3118.0bp to feature; MODIFIER | silent_mutation | Average:54.528; most accessible tissue: Callus, score: 78.52 | N | N | N | N |
| vg0333682687 | C -> T | LOC_Os03g59146.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.528; most accessible tissue: Callus, score: 78.52 | N | N | N | N |
| vg0333682687 | C -> A | LOC_Os03g59152.1 | upstream_gene_variant ; 3118.0bp to feature; MODIFIER | silent_mutation | Average:54.528; most accessible tissue: Callus, score: 78.52 | N | N | N | N |
| vg0333682687 | C -> A | LOC_Os03g59146.1 | intron_variant ; MODIFIER | silent_mutation | Average:54.528; most accessible tissue: Callus, score: 78.52 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0333682687 | 4.86E-07 | 2.57E-06 | mr1192 | 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 |
| vg0333682687 | 1.67E-06 | NA | mr1192 | 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 |
| vg0333682687 | NA | 5.57E-06 | mr1233_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 |
| vg0333682687 | NA | 2.78E-06 | mr1834_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 |