| Variant ID: vg1116002197 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16002197 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 309. )
TACAACTGGAAGATGGAGTGATGCTTCAGGTATCCTGAAATTCCACCTAAAAATGGGAACAAGAACTGCGTCACATCTGCTTTGATCTGATTTGGTTGTT[T/A]
TGCATTACTTTCTTCCATCTAGATTAAGAAATGATTTTGACTCACCCAATATACATGAATATGCAAAACTGTACCCATTCACGCACCAATACACGAAACC
GGTTTCGTGTATTGGTGCGTGAATGGGTACAGTTTTGCATATTCATGTATATTGGGTGAGTCAAAATCATTTCTTAATCTAGATGGAAGAAAGTAATGCA[A/T]
AACAACCAAATCAGATCAAAGCAGATGTGACGCAGTTCTTGTTCCCATTTTTAGGTGGAATTTCAGGATACCTGAAGCATCACTCCATCTTCCAGTTGTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.10% | 5.20% | 1.67% | 0.00% | NA |
| All Indica | 2759 | 88.60% | 8.60% | 2.79% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.30% | 1.20% | 5.55% | 0.00% | NA |
| Indica II | 465 | 83.00% | 13.50% | 3.44% | 0.00% | NA |
| Indica III | 913 | 89.90% | 9.60% | 0.44% | 0.00% | NA |
| Indica Intermediate | 786 | 86.80% | 10.20% | 3.05% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116002197 | T -> A | LOC_Os11g27799.1 | upstream_gene_variant ; 2180.0bp to feature; MODIFIER | silent_mutation | Average:53.353; most accessible tissue: Callus, score: 71.287 | N | N | N | N |
| vg1116002197 | T -> A | LOC_Os11g27795.1 | intron_variant ; MODIFIER | silent_mutation | Average:53.353; most accessible tissue: Callus, score: 71.287 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116002197 | 4.49E-06 | NA | mr1119_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 |
| vg1116002197 | 5.31E-06 | NA | mr1247_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 |