| Variant ID: vg1109858246 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9858246 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGAATTCCCTCCTAATTACCACCTACTACCCAGGTACTAAAAAGAGGGAGTTTCTTCCTCAATTCCCCATCCCCATTCCACCAAAATTCTCATGTATCC[C/T]
AACCAAACAAAGCAGTTAATAGCCTCATCTCTCTAAACTCCCAATCCCTCCTTAAAAACTCCCTCCAACCAAACAGGCCGTAAAGTATTTTTCGTTTAAT
ATTAAACGAAAAATACTTTACGGCCTGTTTGGTTGGAGGGAGTTTTTAAGGAGGGATTGGGAGTTTAGAGAGATGAGGCTATTAACTGCTTTGTTTGGTT[G/A]
GGATACATGAGAATTTTGGTGGAATGGGGATGGGGAATTGAGGAAGAAACTCCCTCTTTTTAGTACCTGGGTAGTAGGTGGTAATTAGGAGGGAATTCCT
| 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 | 41.20% | 3.90% | 0.36% | 54.55% | NA |
| All Indica | 2759 | 14.50% | 6.10% | 0.40% | 79.09% | NA |
| All Japonica | 1512 | 95.60% | 0.80% | 0.13% | 3.44% | NA |
| Aus | 269 | 14.90% | 0.70% | 0.74% | 83.64% | NA |
| Indica I | 595 | 20.30% | 5.90% | 0.50% | 73.28% | NA |
| Indica II | 465 | 10.80% | 0.90% | 1.08% | 87.31% | NA |
| Indica III | 913 | 5.70% | 10.10% | 0.11% | 84.12% | NA |
| Indica Intermediate | 786 | 22.40% | 4.60% | 0.25% | 72.77% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.26% | 3.13% | NA |
| Tropical Japonica | 504 | 94.20% | 2.40% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 95.40% | 0.00% | 0.00% | 4.56% | NA |
| VI/Aromatic | 96 | 21.90% | 0.00% | 1.04% | 77.08% | NA |
| Intermediate | 90 | 44.40% | 4.40% | 1.11% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109858246 | C -> T | LOC_Os11g17660.1 | upstream_gene_variant ; 840.0bp to feature; MODIFIER | silent_mutation | Average:15.479; most accessible tissue: Callus, score: 57.262 | N | N | N | N |
| vg1109858246 | C -> T | LOC_Os11g17670.1 | upstream_gene_variant ; 3764.0bp to feature; MODIFIER | silent_mutation | Average:15.479; most accessible tissue: Callus, score: 57.262 | N | N | N | N |
| vg1109858246 | C -> T | LOC_Os11g17660-LOC_Os11g17670 | intergenic_region ; MODIFIER | silent_mutation | Average:15.479; most accessible tissue: Callus, score: 57.262 | N | N | N | N |
| vg1109858246 | C -> DEL | N | N | silent_mutation | Average:15.479; most accessible tissue: Callus, score: 57.262 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1109858246 | 4.15E-06 | NA | mr1155_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 |