| Variant ID: vg1216702330 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16702330 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.53, G: 0.46, others allele: 0.00, population size: 103. )
CCTATAAAATTTAATTAAAAAGCATAATACTTAGACCTAAATCTTTTTATGTTCGTACAAAAATTTTGAATAAGATGAATGATCAAACGTTTGTAAAAAA[G/T]
TTAACGGGATGACATAGGAGTACATAAAAAATGGAGGTAGTATTTACTCAACTTCCATGACTGCGTCCCAGATTATTGCTTAGTGGATTGTGGGGCCATT
AATGGCCCCACAATCCACTAAGCAATAATCTGGGACGCAGTCATGGAAGTTGAGTAAATACTACCTCCATTTTTTATGTACTCCTATGTCATCCCGTTAA[C/A]
TTTTTTACAAACGTTTGATCATTCATCTTATTCAAAATTTTTGTACGAACATAAAAAGATTTAGGTCTAAGTATTATGCTTTTTAATTAAATTTTATAGG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.30% | 34.80% | 0.25% | 16.61% | NA |
| All Indica | 2759 | 73.00% | 14.00% | 0.22% | 12.76% | NA |
| All Japonica | 1512 | 5.50% | 77.40% | 0.20% | 16.93% | NA |
| Aus | 269 | 53.50% | 14.10% | 0.37% | 31.97% | NA |
| Indica I | 595 | 88.10% | 10.40% | 0.00% | 1.51% | NA |
| Indica II | 465 | 56.10% | 23.90% | 0.65% | 19.35% | NA |
| Indica III | 913 | 73.40% | 12.60% | 0.22% | 13.80% | NA |
| Indica Intermediate | 786 | 71.10% | 12.60% | 0.13% | 16.16% | NA |
| Temperate Japonica | 767 | 5.50% | 94.10% | 0.13% | 0.26% | NA |
| Tropical Japonica | 504 | 4.00% | 49.00% | 0.40% | 46.63% | NA |
| Japonica Intermediate | 241 | 8.70% | 83.40% | 0.00% | 7.88% | NA |
| VI/Aromatic | 96 | 11.50% | 11.50% | 1.04% | 76.04% | NA |
| Intermediate | 90 | 35.60% | 43.30% | 1.11% | 20.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216702330 | G -> DEL | N | N | silent_mutation | Average:47.617; most accessible tissue: Zhenshan97 flower, score: 72.863 | N | N | N | N |
| vg1216702330 | G -> T | LOC_Os12g28260.1 | upstream_gene_variant ; 183.0bp to feature; MODIFIER | silent_mutation | Average:47.617; most accessible tissue: Zhenshan97 flower, score: 72.863 | N | N | N | N |
| vg1216702330 | G -> T | LOC_Os12g28270.1 | downstream_gene_variant ; 4241.0bp to feature; MODIFIER | silent_mutation | Average:47.617; most accessible tissue: Zhenshan97 flower, score: 72.863 | N | N | N | N |
| vg1216702330 | G -> T | LOC_Os12g28270.2 | downstream_gene_variant ; 3226.0bp to feature; MODIFIER | silent_mutation | Average:47.617; most accessible tissue: Zhenshan97 flower, score: 72.863 | N | N | N | N |
| vg1216702330 | G -> T | LOC_Os12g28250-LOC_Os12g28260 | intergenic_region ; MODIFIER | silent_mutation | Average:47.617; most accessible tissue: Zhenshan97 flower, score: 72.863 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216702330 | 1.20E-06 | 1.20E-06 | mr1727 | Jap_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 |
| vg1216702330 | 7.81E-06 | NA | mr1458_2 | 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 |
| vg1216702330 | 4.01E-06 | 3.78E-08 | mr1458_2 | 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 |