| Variant ID: vg1121561200 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21561200 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, T: 0.27, others allele: 0.00, population size: 73. )
AAATAGTATGTAGAATGGTGATTGAAATGTAAAAAGTAAGGTGGTATGACTTTATGGAAGAAGAAAAGTAGAGAGATAGTTTGGACAGTAGATTAATCAT[T/C]
TAAAGGGTAAAAACAATTGATGTGATATGACTTAATTAGAGGAAAAAAGGAGAAAGATAATTTAAACCATAGATTAATCATTTAAGCACTAACTAAGTGA
TCACTTAGTTAGTGCTTAAATGATTAATCTATGGTTTAAATTATCTTTCTCCTTTTTTCCTCTAATTAAGTCATATCACATCAATTGTTTTTACCCTTTA[A/G]
ATGATTAATCTACTGTCCAAACTATCTCTCTACTTTTCTTCTTCCATAAAGTCATACCACCTTACTTTTTACATTTCAATCACCATTCTACATACTATTT
| 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 | 38.10% | 24.70% | 0.17% | 36.99% | NA |
| All Indica | 2759 | 50.30% | 2.50% | 0.22% | 46.90% | NA |
| All Japonica | 1512 | 12.20% | 69.00% | 0.13% | 18.58% | NA |
| Aus | 269 | 67.70% | 10.80% | 0.00% | 21.56% | NA |
| Indica I | 595 | 66.90% | 1.30% | 0.17% | 31.60% | NA |
| Indica II | 465 | 41.90% | 2.40% | 0.43% | 55.27% | NA |
| Indica III | 913 | 46.70% | 1.10% | 0.00% | 52.25% | NA |
| Indica Intermediate | 786 | 47.10% | 5.20% | 0.38% | 47.33% | NA |
| Temperate Japonica | 767 | 11.50% | 79.10% | 0.13% | 9.26% | NA |
| Tropical Japonica | 504 | 15.70% | 55.20% | 0.00% | 29.17% | NA |
| Japonica Intermediate | 241 | 7.50% | 66.00% | 0.41% | 26.14% | NA |
| VI/Aromatic | 96 | 8.30% | 3.10% | 0.00% | 88.54% | NA |
| Intermediate | 90 | 41.10% | 25.60% | 0.00% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121561200 | T -> DEL | N | N | silent_mutation | Average:14.982; most accessible tissue: Callus, score: 36.581 | N | N | N | N |
| vg1121561200 | T -> C | LOC_Os11g36530.1 | upstream_gene_variant ; 4773.0bp to feature; MODIFIER | silent_mutation | Average:14.982; most accessible tissue: Callus, score: 36.581 | N | N | N | N |
| vg1121561200 | T -> C | LOC_Os11g36550.1 | upstream_gene_variant ; 640.0bp to feature; MODIFIER | silent_mutation | Average:14.982; most accessible tissue: Callus, score: 36.581 | N | N | N | N |
| vg1121561200 | T -> C | LOC_Os11g36530-LOC_Os11g36550 | intergenic_region ; MODIFIER | silent_mutation | Average:14.982; most accessible tissue: Callus, score: 36.581 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121561200 | 4.76E-06 | 2.05E-06 | mr1148 | 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 |
| vg1121561200 | 2.87E-06 | NA | mr1409 | 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 |
| vg1121561200 | 5.06E-06 | 5.06E-06 | mr1651 | 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 |
| vg1121561200 | NA | 8.14E-07 | mr1785 | 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 |