Search for Variation information by Variation ID:
Detailed information for vg0315351032:
| Variant ID: vg0315351032 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15351032 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 281. )
Flanking Sequence (100 bp) in Reference Genome:
CTCGATCAGCTATCTGAGGGTCCGATTAAATCCAATATTGATCGGCTCGAAGCTCGCAAGATCGATCTCTTGGCACGGCTTGAAGAATGCAATGCTGAAC[T/C]
GGATATGGAGCACAAAAAGCTAGCCGATCTCCCAAAATCTATCGAAGAACAAAAGGCAAGGCTCAAATCGGCTATTAAGAATGTTGCTGACCTAACCAAG
Reverse complement sequence
CTTGGTTAGGTCAGCAACATTCTTAATAGCCGATTTGAGCCTTGCCTTTTGTTCTTCGATAGATTTTGGGAGATCGGCTAGCTTTTTGTGCTCCATATCC[A/G]
GTTCAGCATTGCATTCTTCAAGCCGTGCCAAGAGATCGATCTTGCGAGCTTCGAGCCGATCAATATTGGATTTAATCGGACCCTCAGATAGCTGATCGAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.00% | 7.00% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 95.80% | 4.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 91.20% | 8.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 1.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.90% | 7.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.90% | 14.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 19.80% | 80.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0315351032 | T -> C | LOC_Os03g26880.1 | missense_variant ; p.Leu744Pro; MODERATE | nonsynonymous_codon ; L744P | Average:36.079; most accessible tissue: Minghui63 panicle, score: 50.413 | probably damaging  |
2.439 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0315351032 | NA | 1.70E-08 | mr1057_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 |
| vg0315351032 | NA | 3.61E-07 | mr1613_2 | Jap_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 |
| vg0315351032 | 5.03E-07 | NA | mr1778_2 | 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 |
| vg0315351032 | NA | 6.20E-07 | mr1913_2 | Jap_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 |
| vg0315351032 | NA | 8.72E-06 | mr1962_2 | Jap_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 |