| Variant ID: vg1123638852 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 23638852 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATGTTGGACACTAGTTATAAATATTAAACGTAGACTATTAATAAAACCCATCCATAATCTTGGACTAATTCGCGAGACGAATCTATTGAGCCTAATTAAT[T/C]
CATGATTAGCTTATGTGATGCTACAGTAAACATTCTCTAATTATAATTAATTAGCCTTAAAAATTTTGTCTCGCAAATTAGCTTTCATTTATGTAATTAG
CTAATTACATAAATGAAAGCTAATTTGCGAGACAAAATTTTTAAGGCTAATTAATTATAATTAGAGAATGTTTACTGTAGCATCACATAAGCTAATCATG[A/G]
ATTAATTAGGCTCAATAGATTCGTCTCGCGAATTAGTCCAAGATTATGGATGGGTTTTATTAATAGTCTACGTTTAATATTTATAACTAGTGTCCAACAT
| 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 | 73.30% | 17.90% | 0.70% | 8.15% | NA |
| All Indica | 2759 | 85.80% | 1.40% | 0.98% | 11.85% | NA |
| All Japonica | 1512 | 49.40% | 48.90% | 0.07% | 1.59% | NA |
| Aus | 269 | 95.90% | 0.70% | 0.37% | 2.97% | NA |
| Indica I | 595 | 89.90% | 2.20% | 0.17% | 7.73% | NA |
| Indica II | 465 | 72.70% | 0.60% | 2.37% | 24.30% | NA |
| Indica III | 913 | 87.70% | 0.40% | 0.99% | 10.84% | NA |
| Indica Intermediate | 786 | 88.20% | 2.30% | 0.76% | 8.78% | NA |
| Temperate Japonica | 767 | 36.50% | 61.00% | 0.13% | 2.35% | NA |
| Tropical Japonica | 504 | 63.30% | 36.10% | 0.00% | 0.60% | NA |
| Japonica Intermediate | 241 | 61.40% | 37.30% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 32.30% | 50.00% | 3.12% | 14.58% | NA |
| Intermediate | 90 | 65.60% | 20.00% | 1.11% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123638852 | T -> DEL | N | N | silent_mutation | Average:26.329; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1123638852 | T -> C | LOC_Os11g39680.1 | downstream_gene_variant ; 2719.0bp to feature; MODIFIER | silent_mutation | Average:26.329; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1123638852 | T -> C | LOC_Os11g39690.1 | downstream_gene_variant ; 1401.0bp to feature; MODIFIER | silent_mutation | Average:26.329; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| vg1123638852 | T -> C | LOC_Os11g39680-LOC_Os11g39690 | intergenic_region ; MODIFIER | silent_mutation | Average:26.329; most accessible tissue: Zhenshan97 panicle, score: 59.59 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1123638852 | NA | 1.45E-07 | mr1829 | 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 |
| vg1123638852 | 4.11E-06 | NA | mr1888 | 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 |
| vg1123638852 | NA | 8.36E-13 | mr1902 | 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 |
| vg1123638852 | NA | 3.73E-09 | mr1829_2 | 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 |
| vg1123638852 | NA | 5.96E-15 | mr1902_2 | 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 |