Search for Variation information by Variation ID:
Detailed information for vg0409515452:
| Variant ID: vg0409515452 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9515452 |
| Reference Allele: C | Alternative Allele: A,T,G |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.00, others allele: 0.00, population size: 232. )
Flanking Sequence (100 bp) in Reference Genome:
TCCTTATCTCTGGTAACCTTAGCAAGGGCTCGTAAACGCGATTGAACCAAGTCCTCCCTCTCATCGGCCATAAGGTTATAATATTCATCGGCTATCAAAC[C/A,T,G]
GTCTTGCAATTCTATCCTTCTAGAGCCGATTCTAACTTCCCATGGCAAAACAGCTTCATGTCCATAAACAAGCTTATAAGGAGGAACTTGAATATTGATC
Reverse complement sequence
GATCAATATTCAAGTTCCTCCTTATAAGCTTGTTTATGGACATGAAGCTGTTTTGCCATGGGAAGTTAGAATCGGCTCTAGAAGGATAGAATTGCAAGAC[G/T,A,C]
GTTTGATAGCCGATGAATATTATAACCTTATGGCCGATGAGAGGGAGGACTTGGTTCAATCGCGTTTACGAGCCCTTGCTAAGGTTACCAGAGATAAGGA
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 | 85.30% | 5.40% | 1.88% | 7.36% | G: 0.02%; T: 0.02% |
| All Indica | 2759 | 96.20% | 3.60% | 0.11% | 0.04% | G: 0.04% |
| All Japonica | 1512 | 74.80% | 0.10% | 3.64% | 21.43% | NA |
| Aus | 269 | 48.00% | 52.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.20% | 0.43% | 0.22% | NA |
| Indica III | 913 | 92.30% | 7.40% | 0.11% | 0.00% | G: 0.11% |
| Indica Intermediate | 786 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.00% | 0.00% | 1.43% | NA |
| Tropical Japonica | 504 | 35.90% | 0.40% | 9.92% | 53.77% | NA |
| Japonica Intermediate | 241 | 80.50% | 0.00% | 2.07% | 17.43% | NA |
| VI/Aromatic | 96 | 34.40% | 12.50% | 30.21% | 22.92% | NA |
| Intermediate | 90 | 92.20% | 3.30% | 2.22% | 1.11% | T: 1.11% |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409515452 | C -> G | LOC_Os04g17380.1 | missense_variant ; p.Gly52Arg; MODERATE | nonsynonymous_codon ; G52R | Average:21.3; most accessible tissue: Callus, score: 28.075 | possibly damaging  |
1.536 |
TOLERATED | 0.09 |
| vg0409515452 | C -> DEL | LOC_Os04g17380.1 | N | frameshift_variant | Average:21.3; most accessible tissue: Callus, score: 28.075 | N | N | N | N |
| vg0409515452 | C -> A | LOC_Os04g17380.1 | missense_variant ; p.Gly52Cys; MODERATE | nonsynonymous_codon ; G52C | Average:21.3; most accessible tissue: Callus, score: 28.075 | probably damaging |
3.035 |
DELETERIOUS | 0.00 |
| vg0409515452 | C -> T | LOC_Os04g17380.1 | missense_variant ; p.Gly52Ser; MODERATE | nonsynonymous_codon ; G52S | Average:21.3; most accessible tissue: Callus, score: 28.075 | benign |
1.092 |
TOLERATED | 0.12 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0409515452 | NA | 2.59E-10 | mr1166_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 |