| Variant ID: vg1218043542 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18043542 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 107. )
CTTTCTCTTCAATAGATTTTGACATACACCTTCCTTGTTAATCAACTTAAACAACCACTTACTCAGGAGACACTTGTTTTGTATTTCCAAGTTATGAACC[C/T]
CTAAACCTCCCTGATCCTTAGGTTGACAAATGATATCCCATCTAGTAAGTCTACTTTTTTTATGGTCATCCCCTTGCCAAAAGAACCATGATCTATAATA
TATTATAGATCATGGTTCTTTTGGCAAGGGGATGACCATAAAAAAAGTAGACTTACTAGATGGGATATCATTTGTCAACCTAAGGATCAGGGAGGTTTAG[G/A]
GGTTCATAACTTGGAAATACAAAACAAGTGTCTCCTGAGTAAGTGGTTGTTTAAGTTGATTAACAAGGAAGGTGTATGTCAAAATCTATTGAAGAGAAAG
| 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 | 59.40% | 39.60% | 1.04% | 0.00% | NA |
| All Indica | 2759 | 42.90% | 55.60% | 1.49% | 0.00% | NA |
| All Japonica | 1512 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 35.30% | 61.70% | 2.97% | 0.00% | NA |
| Indica I | 595 | 48.70% | 50.40% | 0.84% | 0.00% | NA |
| Indica II | 465 | 43.20% | 56.10% | 0.65% | 0.00% | NA |
| Indica III | 913 | 39.10% | 58.60% | 2.30% | 0.00% | NA |
| Indica Intermediate | 786 | 42.60% | 55.90% | 1.53% | 0.00% | NA |
| Temperate Japonica | 767 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 76.30% | 23.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 39.60% | 60.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 31.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1218043542 | C -> T | LOC_Os12g30110.1 | upstream_gene_variant ; 4586.0bp to feature; MODIFIER | silent_mutation | Average:15.179; most accessible tissue: Callus, score: 23.124 | N | N | N | N |
| vg1218043542 | C -> T | LOC_Os12g30120.1 | intron_variant ; MODIFIER | silent_mutation | Average:15.179; most accessible tissue: Callus, score: 23.124 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218043542 | 7.28E-06 | NA | mr1645 | 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 |
| vg1218043542 | 2.38E-06 | NA | mr1647 | 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 |
| vg1218043542 | 4.25E-06 | 4.24E-06 | mr1682 | 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 |