| Variant ID: vg1217798352 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 17798352 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 104. )
CCCTACCCCTATGATCACATTCGAAGAGTAGGCCGGCAAATCCTTGAAATTGACGAAGTCACCATAGGCACCTCGTTGTTGCCTACCACTGAAAGCACAC[C/A]
GCCATTAAATCCTGGAAAATTTGCTCCTATCACTGAAAGCACAACGTTATTAAATCCTGAAAAATTCGCTCTCATGGAGAGTCGAACCCAGGACCTTAGG
CCTAAGGTCCTGGGTTCGACTCTCCATGAGAGCGAATTTTTCAGGATTTAATAACGTTGTGCTTTCAGTGATAGGAGCAAATTTTCCAGGATTTAATGGC[G/T]
GTGTGCTTTCAGTGGTAGGCAACAACGAGGTGCCTATGGTGACTTCGTCAATTTCAAGGATTTGCCGGCCTACTCTTCGAATGTGATCATAGGGGTAGGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 54.60% | 12.50% | 0.55% | 32.33% | NA |
| All Indica | 2759 | 46.40% | 20.60% | 0.47% | 32.48% | NA |
| All Japonica | 1512 | 69.40% | 0.40% | 0.46% | 29.70% | NA |
| Aus | 269 | 61.30% | 0.70% | 0.74% | 37.17% | NA |
| Indica I | 595 | 62.40% | 35.50% | 0.17% | 2.02% | NA |
| Indica II | 465 | 26.70% | 14.40% | 0.86% | 58.06% | NA |
| Indica III | 913 | 45.90% | 11.70% | 0.55% | 41.84% | NA |
| Indica Intermediate | 786 | 46.70% | 23.40% | 0.38% | 29.52% | NA |
| Temperate Japonica | 767 | 95.70% | 0.50% | 0.13% | 3.65% | NA |
| Tropical Japonica | 504 | 40.30% | 0.20% | 0.79% | 58.73% | NA |
| Japonica Intermediate | 241 | 46.90% | 0.40% | 0.83% | 51.87% | NA |
| VI/Aromatic | 96 | 36.50% | 1.00% | 3.12% | 59.38% | NA |
| Intermediate | 90 | 56.70% | 13.30% | 1.11% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1217798352 | C -> DEL | N | N | silent_mutation | Average:29.632; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg1217798352 | C -> A | LOC_Os12g29780.1 | upstream_gene_variant ; 3764.0bp to feature; MODIFIER | silent_mutation | Average:29.632; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| vg1217798352 | C -> A | LOC_Os12g29760-LOC_Os12g29780 | intergenic_region ; MODIFIER | silent_mutation | Average:29.632; most accessible tissue: Zhenshan97 flag leaf, score: 64.768 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1217798352 | NA | 1.61E-06 | mr1180 | 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 |
| vg1217798352 | NA | 4.47E-07 | mr1336 | 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 |
| vg1217798352 | NA | 1.75E-07 | mr1579 | 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 |
| vg1217798352 | 3.39E-06 | NA | mr1458_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 |