Search for Variation information by Variation ID:
Detailed information for vg1124164458:
| Variant ID: vg1124164458 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 24164458 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, A: 0.03, others allele: 0.00, population size: 107. )
Flanking Sequence (100 bp) in Reference Genome:
GGCGTGCCGCTGCCGTCCGACATCGGCGCGCACCTCGGCCGCCTCCTCGCCGCCGGGCACGGCGCGGACGTGGCGATCCACGTTGGCGGCGAGACGTTCG[C/A]
GGCGCACCGGTGCGTGCTCGCCGCGCGGTCGCCGGTGTTCATGGCGGAGCTCTTCGGCCCGATGGCGATGAGCCGTCACAACAACGAGGAGACAATCCGT
Reverse complement sequence
ACGGATTGTCTCCTCGTTGTTGTGACGGCTCATCGCCATCGGGCCGAAGAGCTCCGCCATGAACACCGGCGACCGCGCGGCGAGCACGCACCGGTGCGCC[G/T]
CGAACGTCTCGCCGCCAACGTGGATCGCCACGTCCGCGCCGTGCCCGGCGGCGAGGAGGCGGCCGAGGTGCGCGCCGATGTCGGACGGCAGCGGCACGCC
Allele Frequencies:
| 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 | 92.10% | 7.90% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 88.30% | 11.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.30% | 2.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 84.30% | 15.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.00% | 14.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 86.40% | 13.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1124164458 | C -> A | LOC_Os11g40490.1 | missense_variant ; p.Ala213Glu; MODERATE | nonsynonymous_codon ; A213E | Average:65.271; most accessible tissue: Zhenshan97 panicle, score: 80.486 | benign  |
0.126 |
TOLERATED | 0.11 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1124164458 | 3.65E-06 | NA | mr1111 | 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 |