| Variant ID: vg1205727635 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5727635 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
ATGTGCTATGAAAATCTATACACAGGCTGCATATGATTAAACTATAAACAAGTAAATCGTGTTCAAATCATATTGAGGAATTACTACTGCATGCTCATAT[C/G]
ACTGTCGACTACCACACAACTAATATATATTGTCCTTTGCAGCATCGAAGTGATCAGCTAGCATATCAAACAAATACATCGGTGCATCAATGTATGATTT
AAATCATACATTGATGCACCGATGTATTTGTTTGATATGCTAGCTGATCACTTCGATGCTGCAAAGGACAATATATATTAGTTGTGTGGTAGTCGACAGT[G/C]
ATATGAGCATGCAGTAGTAATTCCTCAATATGATTTGAACACGATTTACTTGTTTATAGTTTAATCATATGCAGCCTGTGTATAGATTTTCATAGCACAT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 96.30% | 1.90% | 1.23% | 0.57% | NA |
| All Indica | 2759 | 94.90% | 3.20% | 1.74% | 0.18% | NA |
| All Japonica | 1512 | 98.10% | 0.00% | 0.53% | 1.39% | NA |
| Aus | 269 | 98.50% | 0.70% | 0.74% | 0.00% | NA |
| Indica I | 595 | 85.00% | 9.10% | 5.71% | 0.17% | NA |
| Indica II | 465 | 97.80% | 0.60% | 1.08% | 0.43% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.90% | 3.70% | 1.15% | 0.25% | NA |
| Temperate Japonica | 767 | 96.50% | 0.00% | 0.91% | 2.61% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205727635 | C -> DEL | N | N | silent_mutation | Average:13.468; most accessible tissue: Zhenshan97 flag leaf, score: 18.943 | N | N | N | N |
| vg1205727635 | C -> G | LOC_Os12g10700.1 | upstream_gene_variant ; 4654.0bp to feature; MODIFIER | silent_mutation | Average:13.468; most accessible tissue: Zhenshan97 flag leaf, score: 18.943 | N | N | N | N |
| vg1205727635 | C -> G | LOC_Os12g10690.1 | downstream_gene_variant ; 301.0bp to feature; MODIFIER | silent_mutation | Average:13.468; most accessible tissue: Zhenshan97 flag leaf, score: 18.943 | N | N | N | N |
| vg1205727635 | C -> G | LOC_Os12g10680-LOC_Os12g10690 | intergenic_region ; MODIFIER | silent_mutation | Average:13.468; most accessible tissue: Zhenshan97 flag leaf, score: 18.943 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1205727635 | 3.60E-06 | 2.24E-07 | mr1198_2 | 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 |
| vg1205727635 | NA | 3.10E-06 | mr1735_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 |
| vg1205727635 | 2.08E-06 | 2.08E-06 | mr1885_2 | 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 |