| Variant ID: vg1209644048 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 9644048 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 93. )
AAATAGAATTGGGCTGAAGTACTGTTTTTAGGCCCAAGCCCATTAGTACTCCTGATACCCTAATAACGCCAAAGAGAAATAAAACGTCTCTTCGTCTTCC[T/C]
CGCCGAGACTCTCGCCACTTTCCCCATTTCCTGCTACAGTGCAAAATTGCGCCGGCAAAGCTAGGGTTCATCGATCTGCTCCAATCCATCCTCCAAAACT
AGTTTTGGAGGATGGATTGGAGCAGATCGATGAACCCTAGCTTTGCCGGCGCAATTTTGCACTGTAGCAGGAAATGGGGAAAGTGGCGAGAGTCTCGGCG[A/G]
GGAAGACGAAGAGACGTTTTATTTCTCTTTGGCGTTATTAGGGTATCAGGAGTACTAATGGGCTTGGGCCTAAAAACAGTACTTCAGCCCAATTCTATTT
| 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 | 67.60% | 27.20% | 1.67% | 3.55% | NA |
| All Indica | 2759 | 92.50% | 4.90% | 0.87% | 1.67% | NA |
| All Japonica | 1512 | 19.00% | 73.00% | 3.37% | 4.63% | NA |
| Aus | 269 | 82.20% | 0.70% | 1.12% | 15.99% | NA |
| Indica I | 595 | 93.90% | 3.50% | 2.02% | 0.50% | NA |
| Indica II | 465 | 87.30% | 12.30% | 0.43% | 0.00% | NA |
| Indica III | 913 | 94.30% | 2.10% | 0.22% | 3.40% | NA |
| Indica Intermediate | 786 | 92.50% | 5.00% | 1.02% | 1.53% | NA |
| Temperate Japonica | 767 | 12.30% | 82.90% | 1.30% | 3.52% | NA |
| Tropical Japonica | 504 | 24.20% | 66.30% | 4.37% | 5.16% | NA |
| Japonica Intermediate | 241 | 29.50% | 55.60% | 7.88% | 7.05% | NA |
| VI/Aromatic | 96 | 86.50% | 7.30% | 0.00% | 6.25% | NA |
| Intermediate | 90 | 55.60% | 40.00% | 1.11% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1209644048 | T -> C | LOC_Os12g16820.1 | upstream_gene_variant ; 191.0bp to feature; MODIFIER | silent_mutation | Average:58.068; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| vg1209644048 | T -> C | LOC_Os12g16830.1 | downstream_gene_variant ; 4342.0bp to feature; MODIFIER | silent_mutation | Average:58.068; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| vg1209644048 | T -> C | LOC_Os12g16810-LOC_Os12g16820 | intergenic_region ; MODIFIER | silent_mutation | Average:58.068; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| vg1209644048 | T -> DEL | N | N | silent_mutation | Average:58.068; most accessible tissue: Minghui63 flag leaf, score: 75.341 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1209644048 | NA | 3.62E-06 | mr1425 | 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 |
| vg1209644048 | 9.44E-07 | 4.00E-11 | mr1425 | 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 |
| vg1209644048 | 3.93E-07 | 1.31E-09 | mr1425_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 |
| vg1209644048 | 3.63E-07 | 2.32E-11 | mr1425_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 |