| Variant ID: vg1126346911 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26346911 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 109. )
AGTTCATACCTTTCACTAACATTGTACCAACCATTACATGTTCCATTTTTATAATATTTTTTAAGTGCTTACATATTAATGGCCTTGCATATATCCTATA[C/T]
CATAGTATTATGAGTTTGTCTGCATATTAAGCCACACTATGGTAGCAGTATACATATAGTTAGTTGAAAAGTTATATTTATTACTATTAAACTTAAATGT
ACATTTAAGTTTAATAGTAATAAATATAACTTTTCAACTAACTATATGTATACTGCTACCATAGTGTGGCTTAATATGCAGACAAACTCATAATACTATG[G/A]
TATAGGATATATGCAAGGCCATTAATATGTAAGCACTTAAAAAATATTATAAAAATGGAACATGTAATGGTTGGTACAATGTTAGTGAAAGGTATGAACT
| 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 | 79.80% | 17.50% | 1.31% | 1.42% | NA |
| All Indica | 2759 | 87.10% | 11.00% | 1.16% | 0.76% | NA |
| All Japonica | 1512 | 67.90% | 29.50% | 1.65% | 0.99% | NA |
| Aus | 269 | 98.90% | 0.70% | 0.00% | 0.37% | NA |
| Indica I | 595 | 83.50% | 15.50% | 0.67% | 0.34% | NA |
| Indica II | 465 | 92.90% | 5.40% | 1.51% | 0.22% | NA |
| Indica III | 913 | 90.90% | 7.10% | 0.55% | 1.42% | NA |
| Indica Intermediate | 786 | 81.80% | 15.50% | 2.04% | 0.64% | NA |
| Temperate Japonica | 767 | 54.20% | 43.50% | 2.09% | 0.13% | NA |
| Tropical Japonica | 504 | 86.30% | 9.90% | 1.39% | 2.38% | NA |
| Japonica Intermediate | 241 | 72.60% | 25.70% | 0.83% | 0.83% | NA |
| VI/Aromatic | 96 | 8.30% | 60.40% | 3.12% | 28.12% | NA |
| Intermediate | 90 | 75.60% | 18.90% | 2.22% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126346911 | C -> T | LOC_Os11g43660.1 | upstream_gene_variant ; 3875.0bp to feature; MODIFIER | silent_mutation | Average:26.867; most accessible tissue: Zhenshan97 young leaf, score: 42.553 | N | N | N | N |
| vg1126346911 | C -> T | LOC_Os11g43650-LOC_Os11g43660 | intergenic_region ; MODIFIER | silent_mutation | Average:26.867; most accessible tissue: Zhenshan97 young leaf, score: 42.553 | N | N | N | N |
| vg1126346911 | C -> DEL | N | N | silent_mutation | Average:26.867; most accessible tissue: Zhenshan97 young leaf, score: 42.553 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1126346911 | NA | 1.43E-06 | mr1585 | 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 |
| vg1126346911 | NA | 5.26E-07 | mr1739 | 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 |
| vg1126346911 | NA | 1.48E-06 | mr1765 | 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 |
| vg1126346911 | 4.91E-06 | 4.91E-06 | mr1899 | 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 |
| vg1126346911 | NA | 9.13E-06 | mr1582_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 |