Search for Variation information by Variation ID:
Detailed information for vg0334746454:
| Variant ID: vg0334746454 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 34746454 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )
Flanking Sequence (100 bp) in Reference Genome:
CTCTTGTCATGCAAAAAGAACACCCACGTGAAGCGTGAAAAGTCATCAACAATAACAAGACCATATTTGTTACCTCCAATGCTTAGATAAGCAATTGGTC[C/T]
GAAGAGGTCCATGTGGAGAAGCTCCAATGGTCTTGTAGTTGTCATCACATTCTTGTCGGGCGATGTGCTCTAATTTGTTTGCCGGCTTGACATGCACTAC
Reverse complement sequence
GTAGTGCATGTCAAGCCGGCAAACAAATTAGAGCACATCGCCCGACAAGAATGTGATGACAACTACAAGACCATTGGAGCTTCTCCACATGGACCTCTTC[G/A]
GACCAATTGCTTATCTAAGCATTGGAGGTAACAAATATGGTCTTGTTATTGTTGATGACTTTTCACGCTTCACGTGGGTGTTCTTTTTGCATGACAAGAG
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 | 50.60% | 49.40% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 75.80% | 24.20% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 2.00% | 98.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 79.90% | 20.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica II | 465 | 87.30% | 12.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 56.10% | 43.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 76.00% | 24.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 4.20% | 95.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 1.70% | 98.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 15.60% | 84.40% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 43.30% | 55.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0334746454 | C -> T | LOC_Os03g61180.1 | missense_variant ; p.Gly826Arg; MODERATE | nonsynonymous_codon ; G826R | Average:14.86; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
0.767 |
DELETERIOUS | 0.05 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0334746454 | NA | 2.20E-10 | Heading_date | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0334746454 | 7.54E-06 | NA | mr1114_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 |
| vg0334746454 | 4.61E-06 | NA | mr1117_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 |
| vg0334746454 | 5.00E-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 |
| vg0334746454 | 5.42E-06 | NA | mr1842_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 |