| Variant ID: vg1112963070 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 12963070 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AACCTTGTCCAACTCAGACTCCGCCGATCCTGGTCGCAGCCGATCTCCATCTCGGATTCTGCTTCGACTTTATCACTGTCACGCTAGGAATTTCTATCCA[C/A]
AATTCCAAACGCTTACATGTGCGTTAAATCCTCATCCAGGAATCAGCCGAGGCACACAATAACAAATTGATAAAAGAGTACTATCAAACTACTGATTAAT
ATTAATCAGTAGTTTGATAGTACTCTTTTATCAATTTGTTATTGTGTGCCTCGGCTGATTCCTGGATGAGGATTTAACGCACATGTAAGCGTTTGGAATT[G/T]
TGGATAGAAATTCCTAGCGTGACAGTGATAAAGTCGAAGCAGAATCCGAGATGGAGATCGGCTGCGACCAGGATCGGCGGAGTCTGAGTTGGACAAGGTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 63.20% | 1.00% | 3.20% | 32.61% | NA |
| All Indica | 2759 | 40.60% | 1.30% | 5.00% | 53.10% | NA |
| All Japonica | 1512 | 97.20% | 0.10% | 0.07% | 2.65% | NA |
| Aus | 269 | 88.80% | 3.70% | 4.09% | 3.35% | NA |
| Indica I | 595 | 63.00% | 0.80% | 1.51% | 34.62% | NA |
| Indica II | 465 | 37.20% | 0.40% | 0.43% | 61.94% | NA |
| Indica III | 913 | 25.60% | 2.10% | 8.54% | 63.75% | NA |
| Indica Intermediate | 786 | 43.00% | 1.30% | 6.23% | 49.49% | NA |
| Temperate Japonica | 767 | 99.30% | 0.10% | 0.00% | 0.52% | NA |
| Tropical Japonica | 504 | 93.50% | 0.00% | 0.00% | 6.55% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.40% | 0.41% | 1.24% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 72.20% | 0.00% | 1.11% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1112963070 | C -> A | LOC_Os11g22540.1 | downstream_gene_variant ; 2548.0bp to feature; MODIFIER | silent_mutation | Average:12.134; most accessible tissue: Callus, score: 33.087 | N | N | N | N |
| vg1112963070 | C -> A | LOC_Os11g22550.1 | downstream_gene_variant ; 1353.0bp to feature; MODIFIER | silent_mutation | Average:12.134; most accessible tissue: Callus, score: 33.087 | N | N | N | N |
| vg1112963070 | C -> A | LOC_Os11g22540-LOC_Os11g22550 | intergenic_region ; MODIFIER | silent_mutation | Average:12.134; most accessible tissue: Callus, score: 33.087 | N | N | N | N |
| vg1112963070 | C -> DEL | N | N | silent_mutation | Average:12.134; most accessible tissue: Callus, score: 33.087 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1112963070 | NA | 3.48E-06 | mr1125_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 |
| vg1112963070 | 2.69E-06 | NA | mr1165_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 |
| vg1112963070 | 2.84E-06 | NA | mr1522_2 | 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 |
| vg1112963070 | 6.24E-06 | 4.69E-07 | mr1522_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 |
| vg1112963070 | NA | 5.43E-06 | mr1553_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 |