| Variant ID: vg0135567772 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 35567772 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.03, others allele: 0.00, population size: 32. )
CCGGTCTGACCGGCCACCCCATGCCGGTCTGACCAGCCAGGCCGTTGGGGCCCTCTGACAGGGCTACAACAGCTAGTTTTCTAGCCGTTGCAGAGTAGCA[C/T]
GGTCTGACCGGCCACATACCTCCGATCAGACCGGCAGAGCACAGAGTTAGGGGATTTCGCCCCCAACGACTAGTTTTGGTGGGTGGGAGTATAAATACTC
GAGTATTTATACTCCCACCCACCAAAACTAGTCGTTGGGGGCGAAATCCCCTAACTCTGTGCTCTGCCGGTCTGATCGGAGGTATGTGGCCGGTCAGACC[G/A]
TGCTACTCTGCAACGGCTAGAAAACTAGCTGTTGTAGCCCTGTCAGAGGGCCCCAACGGCCTGGCTGGTCAGACCGGCATGGGGTGGCCGGTCAGACCGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.00% | 36.60% | 7.07% | 5.31% | NA |
| All Indica | 2759 | 82.00% | 1.20% | 7.94% | 8.84% | NA |
| All Japonica | 1512 | 1.50% | 98.30% | 0.13% | 0.07% | NA |
| Aus | 269 | 36.10% | 22.70% | 39.78% | 1.49% | NA |
| Indica I | 595 | 73.40% | 0.70% | 9.92% | 15.97% | NA |
| Indica II | 465 | 91.40% | 0.90% | 2.80% | 4.95% | NA |
| Indica III | 913 | 84.80% | 1.00% | 7.34% | 6.90% | NA |
| Indica Intermediate | 786 | 79.60% | 2.20% | 10.18% | 8.02% | NA |
| Temperate Japonica | 767 | 1.00% | 98.80% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 2.00% | 97.80% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 1.70% | 97.90% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 2.10% | 96.90% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 31.10% | 61.10% | 5.56% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0135567772 | C -> T | LOC_Os01g61490.1 | upstream_gene_variant ; 879.0bp to feature; MODIFIER | silent_mutation | Average:18.052; most accessible tissue: Callus, score: 24.739 | N | N | N | N |
| vg0135567772 | C -> T | LOC_Os01g61480-LOC_Os01g61490 | intergenic_region ; MODIFIER | silent_mutation | Average:18.052; most accessible tissue: Callus, score: 24.739 | N | N | N | N |
| vg0135567772 | C -> DEL | N | N | silent_mutation | Average:18.052; most accessible tissue: Callus, score: 24.739 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0135567772 | 3.91E-06 | NA | mr1015 | 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 |
| vg0135567772 | 3.08E-06 | NA | mr1015 | 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 |
| vg0135567772 | 6.64E-06 | NA | mr1116 | 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 |
| vg0135567772 | NA | 8.39E-12 | mr1553 | 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 |
| vg0135567772 | 6.27E-06 | 2.66E-12 | mr1623 | 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 |
| vg0135567772 | NA | 1.82E-07 | mr1781 | 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 |