| Variant ID: vg1103603230 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 3603230 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, T: 0.06, others allele: 0.00, population size: 81. )
TGTTTTTCCTGTGTTTTGCAATCCTCTGTTTTACACTTACATTCCTATCAAAATCCTGCGTTTTTTCTATTCCTATGTTTTCTCATTCCTGCGATTCAAA[G/T]
GGGCCCTGACTATGTCAATGGCCATAAACCACACGTTTATGATTACGTTAGATACGCAACCTAACCAATATAAGGATGTTAGATGGTATATTTTTTTTAA
TTAAAAAAAATATACCATCTAACATCCTTATATTGGTTAGGTTGCGTATCTAACGTAATCATAAACGTGTGGTTTATGGCCATTGACATAGTCAGGGCCC[C/A]
TTTGAATCGCAGGAATGAGAAAACATAGGAATAGAAAAAACGCAGGATTTTGATAGGAATGTAAGTGTAAAACAGAGGATTGCAAAACACAGGAAAAACA
| 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 | 47.10% | 31.30% | 0.11% | 21.50% | NA |
| All Indica | 2759 | 59.90% | 7.50% | 0.18% | 32.44% | NA |
| All Japonica | 1512 | 18.20% | 79.30% | 0.00% | 2.51% | NA |
| Aus | 269 | 71.40% | 3.00% | 0.00% | 25.65% | NA |
| Indica I | 595 | 34.60% | 1.50% | 0.17% | 63.70% | NA |
| Indica II | 465 | 85.60% | 4.90% | 0.00% | 9.46% | NA |
| Indica III | 913 | 67.80% | 9.50% | 0.00% | 22.67% | NA |
| Indica Intermediate | 786 | 54.70% | 11.10% | 0.51% | 33.72% | NA |
| Temperate Japonica | 767 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 44.80% | 48.20% | 0.00% | 6.94% | NA |
| Japonica Intermediate | 241 | 12.00% | 86.70% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 58.30% | 40.60% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 56.70% | 28.90% | 0.00% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1103603230 | G -> T | LOC_Os11g07200.1 | upstream_gene_variant ; 3789.0bp to feature; MODIFIER | silent_mutation | Average:40.095; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| vg1103603230 | G -> T | LOC_Os11g07200.2 | upstream_gene_variant ; 3789.0bp to feature; MODIFIER | silent_mutation | Average:40.095; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| vg1103603230 | G -> T | LOC_Os11g07190-LOC_Os11g07200 | intergenic_region ; MODIFIER | silent_mutation | Average:40.095; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| vg1103603230 | G -> DEL | N | N | silent_mutation | Average:40.095; most accessible tissue: Minghui63 root, score: 49.234 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1103603230 | NA | 5.44E-06 | mr1088 | 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 |
| vg1103603230 | NA | 2.09E-06 | mr1104 | 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 |
| vg1103603230 | 7.28E-07 | 1.45E-12 | mr1241 | 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 |
| vg1103603230 | NA | 9.47E-09 | mr1593 | 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 |