| Variant ID: vg0223701961 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 23701961 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 286. )
TAGAAACCAAATGCGAAAAATGTCATAGGAGATCCAAACACAATGACGTCATTGAGAGTCGTAGCTTATATCCCCGAGGCACTGATAACGGGTACACATC[C/T]
CCGATCCAACATATTACAGCGTATATATCAGAGTTACAGCAACCCTTGGCCGAACGTCGCTGGCAGCCGCTCCCTCTCGCTATGCTAAGTCGCCATGTCG
CGACATGGCGACTTAGCATAGCGAGAGGGAGCGGCTGCCAGCGACGTTCGGCCAAGGGTTGCTGTAACTCTGATATATACGCTGTAATATGTTGGATCGG[G/A]
GATGTGTACCCGTTATCAGTGCCTCGGGGATATAAGCTACGACTCTCAATGACGTCATTGTGTTTGGATCTCCTATGACATTTTTCGCATTTGGTTTCTA
| 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 | 66.60% | 31.80% | 1.57% | 0.00% | NA |
| All Indica | 2759 | 58.90% | 40.10% | 0.98% | 0.00% | NA |
| All Japonica | 1512 | 73.20% | 24.10% | 2.71% | 0.00% | NA |
| Aus | 269 | 98.10% | 1.10% | 0.74% | 0.00% | NA |
| Indica I | 595 | 41.00% | 56.80% | 2.18% | 0.00% | NA |
| Indica II | 465 | 59.60% | 40.20% | 0.22% | 0.00% | NA |
| Indica III | 913 | 75.90% | 24.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 52.30% | 46.20% | 1.53% | 0.00% | NA |
| Temperate Japonica | 767 | 88.80% | 8.30% | 2.87% | 0.00% | NA |
| Tropical Japonica | 504 | 57.90% | 40.30% | 1.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 55.60% | 40.20% | 4.15% | 0.00% | NA |
| VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 30.00% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0223701961 | C -> T | LOC_Os02g39240.1 | upstream_gene_variant ; 3697.0bp to feature; MODIFIER | silent_mutation | Average:42.93; most accessible tissue: Callus, score: 78.717 | N | N | N | N |
| vg0223701961 | C -> T | LOC_Os02g39220.1 | downstream_gene_variant ; 3780.0bp to feature; MODIFIER | silent_mutation | Average:42.93; most accessible tissue: Callus, score: 78.717 | N | N | N | N |
| vg0223701961 | C -> T | LOC_Os02g39230.1 | downstream_gene_variant ; 331.0bp to feature; MODIFIER | silent_mutation | Average:42.93; most accessible tissue: Callus, score: 78.717 | N | N | N | N |
| vg0223701961 | C -> T | LOC_Os02g39230-LOC_Os02g39240 | intergenic_region ; MODIFIER | silent_mutation | Average:42.93; most accessible tissue: Callus, score: 78.717 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0223701961 | NA | 4.76E-06 | mr1157 | 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 |
| vg0223701961 | NA | 1.07E-06 | mr1163 | 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 |
| vg0223701961 | 8.54E-07 | 8.53E-07 | mr1184 | 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 |
| vg0223701961 | NA | 1.40E-07 | mr1617 | 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 |