| Variant ID: vg1109845531 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9845531 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.89, T: 0.11, others allele: 0.00, population size: 45. )
TATAAACCAGTACCTATTGTCTCGGGCCGGAACACACGTCATTAAGATAATAGGTGCCCGTTTTTTACGAACGGCCGTCACCTATACTTTTTTAGACCAT[C/T]
GGCGGGAGGGCCTTCGGTGCCTCTCTCAAAGAACCGGGACCTATTAAACATTATAGCTGCCGGTTATAGAAATGGTGGGTGAGAAACGGCTTATAGGTGT
ACACCTATAAGCCGTTTCTCACCCACCATTTCTATAACCGGCAGCTATAATGTTTAATAGGTCCCGGTTCTTTGAGAGAGGCACCGAAGGCCCTCCCGCC[G/A]
ATGGTCTAAAAAAGTATAGGTGACGGCCGTTCGTAAAAAACGGGCACCTATTATCTTAATGACGTGTGTTCCGGCCCGAGACAATAGGTACTGGTTTATA
| 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 | 35.60% | 22.40% | 1.67% | 40.37% | NA |
| All Indica | 2759 | 5.90% | 28.40% | 2.03% | 63.72% | NA |
| All Japonica | 1512 | 95.60% | 1.50% | 0.20% | 2.65% | NA |
| Aus | 269 | 8.90% | 81.80% | 4.46% | 4.83% | NA |
| Indica I | 595 | 4.00% | 18.80% | 0.84% | 76.30% | NA |
| Indica II | 465 | 1.50% | 8.20% | 0.43% | 89.89% | NA |
| Indica III | 913 | 2.00% | 50.20% | 1.75% | 46.11% | NA |
| Indica Intermediate | 786 | 14.40% | 22.30% | 4.20% | 59.16% | NA |
| Temperate Japonica | 767 | 97.00% | 0.10% | 0.00% | 2.87% | NA |
| Tropical Japonica | 504 | 93.80% | 4.20% | 0.40% | 1.59% | NA |
| Japonica Intermediate | 241 | 95.00% | 0.40% | 0.41% | 4.15% | NA |
| VI/Aromatic | 96 | 19.80% | 12.50% | 4.17% | 63.54% | NA |
| Intermediate | 90 | 34.40% | 21.10% | 4.44% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109845531 | C -> T | LOC_Os11g17640.1 | downstream_gene_variant ; 2782.0bp to feature; MODIFIER | silent_mutation | Average:52.183; most accessible tissue: Callus, score: 62.937 | N | N | N | N |
| vg1109845531 | C -> T | LOC_Os11g17640-LOC_Os11g17650 | intergenic_region ; MODIFIER | silent_mutation | Average:52.183; most accessible tissue: Callus, score: 62.937 | N | N | N | N |
| vg1109845531 | C -> DEL | N | N | silent_mutation | Average:52.183; most accessible tissue: Callus, score: 62.937 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1109845531 | 2.30E-06 | NA | mr1154 | 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 |
| vg1109845531 | NA | 8.05E-12 | mr1522 | 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 |
| vg1109845531 | NA | 7.53E-07 | mr1574 | 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 |
| vg1109845531 | NA | 8.64E-09 | mr1388_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 |