| Variant ID: vg1108111928 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8111928 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.13, others allele: 0.00, population size: 45. )
ACCCAGAAATTTCCAGCGGTCATCTCTCCTTTCCTTGGAATTCGCACCATCGGTAGTGCGTCTATTTAAGGAAGTTTTGGGGATCCATTTTGAAGTCCGC[T/C]
TGTTGCGAAAAACTCTCCAGCCTCCAAGCGTTCCTCTTCTTCTCCGCTCCCGCAAAAACCCTAGCTTGCTCATCTCGGTCCTTTCTCCGGCGACCTCCGG
CCGGAGGTCGCCGGAGAAAGGACCGAGATGAGCAAGCTAGGGTTTTTGCGGGAGCGGAGAAGAAGAGGAACGCTTGGAGGCTGGAGAGTTTTTCGCAACA[A/G]
GCGGACTTCAAAATGGATCCCCAAAACTTCCTTAAATAGACGCACTACCGATGGTGCGAATTCCAAGGAAAGGAGAGATGACCGCTGGAAATTTCTGGGT
| 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 | 54.00% | 37.00% | 4.44% | 4.57% | NA |
| All Indica | 2759 | 86.30% | 5.10% | 6.63% | 1.99% | NA |
| All Japonica | 1512 | 2.60% | 88.50% | 1.06% | 7.87% | NA |
| Aus | 269 | 27.50% | 59.50% | 2.60% | 10.41% | NA |
| Indica I | 595 | 75.10% | 6.20% | 15.29% | 3.36% | NA |
| Indica II | 465 | 94.20% | 2.20% | 1.94% | 1.72% | NA |
| Indica III | 913 | 90.60% | 3.90% | 4.82% | 0.66% | NA |
| Indica Intermediate | 786 | 85.10% | 7.30% | 4.96% | 2.67% | NA |
| Temperate Japonica | 767 | 0.70% | 95.60% | 1.56% | 2.22% | NA |
| Tropical Japonica | 504 | 5.20% | 80.20% | 0.60% | 14.09% | NA |
| Japonica Intermediate | 241 | 3.30% | 83.40% | 0.41% | 12.86% | NA |
| VI/Aromatic | 96 | 10.40% | 79.20% | 2.08% | 8.33% | NA |
| Intermediate | 90 | 51.10% | 40.00% | 2.22% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108111928 | T -> DEL | N | N | silent_mutation | Average:22.264; most accessible tissue: Callus, score: 52.883 | N | N | N | N |
| vg1108111928 | T -> C | LOC_Os11g14450.1 | upstream_gene_variant ; 106.0bp to feature; MODIFIER | silent_mutation | Average:22.264; most accessible tissue: Callus, score: 52.883 | N | N | N | N |
| vg1108111928 | T -> C | LOC_Os11g14440.1 | downstream_gene_variant ; 4589.0bp to feature; MODIFIER | silent_mutation | Average:22.264; most accessible tissue: Callus, score: 52.883 | N | N | N | N |
| vg1108111928 | T -> C | LOC_Os11g14460.1 | downstream_gene_variant ; 3023.0bp to feature; MODIFIER | silent_mutation | Average:22.264; most accessible tissue: Callus, score: 52.883 | N | N | N | N |
| vg1108111928 | T -> C | LOC_Os11g14440-LOC_Os11g14450 | intergenic_region ; MODIFIER | silent_mutation | Average:22.264; most accessible tissue: Callus, score: 52.883 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108111928 | NA | 3.67E-06 | mr1058 | 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 |
| vg1108111928 | 8.86E-07 | 8.86E-07 | mr1918 | 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 |
| vg1108111928 | NA | 7.71E-06 | mr1761_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 |