Search for Variation information by Variation ID:
Detailed information for vg0228295621:
| Variant ID: vg0228295621 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 28295621 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
AGATTAAAGTTTGGTCTGAAGTTTGTCATGGACCAGTTCTCGCTGAGTCTGCCAGGTTTCTGGAGTGTGTTAGAGTAACTCATAACACAGTGGGACTCAC[A/G]
GGCAGACTTCGATCTCCAAACAGATGAAAGAACAGCCATGAAATGTTTCTGGAGAAGCAATTCATTGTTAGGAAGCTCGCTGATTACATTGAGCAACATC
Reverse complement sequence
GATGTTGCTCAATGTAATCAGCGAGCTTCCTAACAATGAATTGCTTCTCCAGAAACATTTCATGGCTGTTCTTTCATCTGTTTGGAGATCGAAGTCTGCC[T/C]
GTGAGTCCCACTGTGTTATGAGTTACTCTAACACACTCCAGAAACCTGGCAGACTCAGCGAGAACTGGTCCATGACAAACTTCAGACCAAACTTTAATCT
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.40% | 38.60% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 0.70% | 99.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 59.10% | 40.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 1.20% | 98.80% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 0.40% | 99.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 1.00% | 99.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 41.10% | 58.90% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0228295621 | A -> G | LOC_Os02g46450.1 | missense_variant ; p.Cys805Arg; MODERATE | nonsynonymous_codon ; C805R | Average:62.214; most accessible tissue: Zhenshan97 flower, score: 74.459 | probably damaging  |
-3.064 |
TOLERATED | 0.40 |
| vg0228295621 | A -> G | LOC_Os02g46450.2 | missense_variant ; p.Cys805Arg; MODERATE | nonsynonymous_codon ; C805R | Average:62.214; most accessible tissue: Zhenshan97 flower, score: 74.459 | probably damaging |
-3.16 |
TOLERATED | 0.40 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0228295621 | NA | 2.98E-10 | mr1342 | 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 |
| vg0228295621 | 3.42E-11 | 9.83E-89 | mr1629 | 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 |
| vg0228295621 | 5.13E-06 | 8.55E-12 | mr1905 | 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 |
| vg0228295621 | NA | 1.36E-75 | mr1246_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 |
| vg0228295621 | NA | 6.12E-18 | mr1342_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 |
| vg0228295621 | 8.52E-10 | 1.38E-107 | mr1629_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 |
| vg0228295621 | NA | 5.49E-77 | mr1671_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 |
| vg0228295621 | 9.26E-06 | 1.38E-08 | mr1905_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 |
| vg0228295621 | NA | 2.39E-40 | mr1944_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 |