| Variant ID: vg1212666777 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 12666777 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.14, others allele: 0.00, population size: 72. )
ATCGGAGTTATGGAATAAGATAGACTGCAGTTTACCTATTCCCTTTTTCTTTCTAGCTGTTCCGAATCTCGGGACGAGATTCTTTGTAAGGGGGGTAGAT[C/T]
TGTCACATCCTGATTTTCATTTTAGGATTTATAAATTATTTAATAAATTATTAATAGAATTTATATTAAATGATCTTTAATTTACAAGTGAAGTTAAAGG
CCTTTAACTTCACTTGTAAATTAAAGATCATTTAATATAAATTCTATTAATAATTTATTAAATAATTTATAAATCCTAAAATGAAAATCAGGATGTGACA[G/A]
ATCTACCCCCCTTACAAAGAATCTCGTCCCGAGATTCGGAACAGCTAGAAAGAAAAAGGGAATAGGTAAACTGCAGTCTATCTTATTCCATAACTCCGAT
| 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 | 17.40% | 5.60% | 14.05% | 62.95% | NA |
| All Indica | 2759 | 4.30% | 9.40% | 19.83% | 66.44% | NA |
| All Japonica | 1512 | 44.00% | 0.00% | 1.52% | 54.50% | NA |
| Aus | 269 | 3.30% | 1.10% | 28.25% | 67.29% | NA |
| Indica I | 595 | 1.00% | 6.10% | 11.09% | 81.85% | NA |
| Indica II | 465 | 3.20% | 7.50% | 17.85% | 71.40% | NA |
| Indica III | 913 | 5.00% | 13.50% | 26.73% | 54.76% | NA |
| Indica Intermediate | 786 | 6.60% | 8.40% | 19.59% | 65.39% | NA |
| Temperate Japonica | 767 | 77.20% | 0.00% | 0.65% | 22.16% | NA |
| Tropical Japonica | 504 | 3.20% | 0.00% | 2.18% | 94.64% | NA |
| Japonica Intermediate | 241 | 23.70% | 0.00% | 2.90% | 73.44% | NA |
| VI/Aromatic | 96 | 3.10% | 1.00% | 8.33% | 87.50% | NA |
| Intermediate | 90 | 27.80% | 2.20% | 11.11% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212666777 | C -> DEL | N | N | silent_mutation | Average:9.155; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666777 | C -> T | LOC_Os12g22430.1 | downstream_gene_variant ; 309.0bp to feature; MODIFIER | silent_mutation | Average:9.155; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666777 | C -> T | LOC_Os12g22440.1 | downstream_gene_variant ; 3660.0bp to feature; MODIFIER | silent_mutation | Average:9.155; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1212666777 | C -> T | LOC_Os12g22430-LOC_Os12g22440 | intergenic_region ; MODIFIER | silent_mutation | Average:9.155; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1212666777 | NA | 7.34E-06 | mr1414 | 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 |
| vg1212666777 | 1.28E-06 | 1.28E-06 | mr1703 | 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 |
| vg1212666777 | NA | 4.99E-07 | mr1763 | 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 |
| vg1212666777 | NA | 1.62E-06 | mr1558_2 | 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 |