Search for Variation information by Variation ID:
Detailed information for vg0401256484:
| Variant ID: vg0401256484 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1256484 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, G: 0.06, others allele: 0.00, population size: 209. )
Flanking Sequence (100 bp) in Reference Genome:
TCCCAGTTGTATACTCTGCTGGGAACGATGGACCCGTTGCTCAGACAGTGGAGAACTCATCACCATGGCTGTTAACGGTTGCTGCAGCCACCATGGATCG[A/G]
TCCTTCCCTGTGGTTATCACCTTGGGCGATAATCATAAGTTTGTGGTATATATATATTATGTGCAGTTCATTCATTCTGACTTAAATTGGATATATATCC
Reverse complement sequence
GGATATATATCCAATTTAAGTCAGAATGAATGAACTGCACATAATATATATATACCACAAACTTATGATTATCGCCCAAGGTGATAACCACAGGGAAGGA[T/C]
CGATCCATGGTGGCTGCAGCAACCGTTAACAGCCATGGTGATGAGTTCTCCACTGTCTGAGCAACGGGTCCATCGTTCCCAGCAGAGTATACAACTGGGA
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 | 84.20% | 15.70% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 89.90% | 10.00% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 70.40% | 29.50% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 1.30% | 0.17% | 0.00% | NA |
| Indica II | 465 | 79.80% | 20.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 85.70% | 14.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 94.30% | 5.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 60.60% | 39.20% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 78.20% | 21.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 85.50% | 14.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 82.20% | 16.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0401256484 | A -> G | LOC_Os04g03050.1 | synonymous_variant ; p.Arg341Arg; LOW | synonymous_codon | Average:60.308; most accessible tissue: Callus, score: 81.069 | N | N | N | N |
| vg0401256484 | A -> G | LOC_Os04g03050.1 | synonymous_variant ; p.Arg341Arg; LOW | nonsynonymous_codon ; R341Q | Average:60.308; most accessible tissue: Callus, score: 81.069 | benign  |
0.93 |
DELETERIOUS | 0.01 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401256484 | NA | 6.45E-10 | Heading_date | Jap_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 |
| vg0401256484 | 2.07E-06 | NA | mr1565_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 |