Search for Variation information by Variation ID:
Detailed information for vg1116407848:
| Variant ID: vg1116407848 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16407848 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 53. )
Flanking Sequence (100 bp) in Reference Genome:
TTGGCAACGCTGAGCATCTCCTTAGGCGAGTAACCATCGCCGTCCCGGTAGAAGGCACTTGCCACATTACTCGTCTGCCAGAACATCTCCCTGCACGACC[G/A]
GGGAACAACCCCGGCGCCGTCTCCGAACACCAGCCTCTGCAGCTCCCCCCTCAACGCCCGGATGGCCCTCCCGATCTCCACCTTGGCCGCCTCCACGGAC
Reverse complement sequence
GTCCGTGGAGGCGGCCAAGGTGGAGATCGGGAGGGCCATCCGGGCGTTGAGGGGGGAGCTGCAGAGGCTGGTGTTCGGAGACGGCGCCGGGGTTGTTCCC[C/T]
GGTCGTGCAGGGAGATGTTCTGGCAGACGAGTAATGTGGCAAGTGCCTTCTACCGGGACGGCGATGGTTACTCGCCTAAGGAGATGCTCAGCGTTGCCAA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 56.10% | 43.80% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 87.70% | 12.20% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 2.00% | 97.90% | 0.07% | 0.00% | NA |
| Aus | 269 | 55.80% | 44.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 90.60% | 9.20% | 0.17% | 0.00% | NA |
| Indica II | 465 | 94.80% | 4.90% | 0.22% | 0.00% | NA |
| Indica III | 913 | 84.90% | 15.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 84.60% | 15.40% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 2.20% | 97.60% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 8.30% | 91.70% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 47.80% | 51.10% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116407848 | G -> A | LOC_Os11g28490.1 | missense_variant ; p.Arg172Trp; MODERATE | nonsynonymous_codon ; R172W | Average:60.166; most accessible tissue: Minghui63 panicle, score: 83.421 | benign  |
0.338 |
TOLERATED | 0.08 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116407848 | NA | 3.12E-12 | mr1595 | 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 |