Search for Variation information by Variation ID:
Detailed information for vg0801342227:
| Variant ID: vg0801342227 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 1342227 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 97. )
Flanking Sequence (100 bp) in Reference Genome:
GGAGTCTTTGGCGAACCTCTTTATGGCAACGTCTAGGCCGAGCTCTCTCAGATTGCCACGGTACACCGCGCCGAAACCGCCTTGCCCAAGCTTCTCCTCC[G/T]
CCGCAAAGCTCTTTGTCGCGTTGACAAGTATGTGGTACGGGAACCGCCTCGGCCCCGTCCCCATCTCGATCTCCACGATGGGATCGCCTTCCGAGTCGTC
Reverse complement sequence
GACGACTCGGAAGGCGATCCCATCGTGGAGATCGAGATGGGGACGGGGCCGAGGCGGTTCCCGTACCACATACTTGTCAACGCGACAAAGAGCTTTGCGG[C/A]
GGAGGAGAAGCTTGGGCAAGGCGGTTTCGGCGCGGTGTACCGTGGCAATCTGAGAGAGCTCGGCCTAGACGTTGCCATAAAGAGGTTCGCCAAAGACTCC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 47.40% | 19.70% | 1.69% | 31.17% | NA |
| All Indica | 2759 | 25.30% | 24.50% | 2.32% | 47.81% | NA |
| All Japonica | 1512 | 97.60% | 0.50% | 0.13% | 1.79% | NA |
| Aus | 269 | 3.00% | 82.90% | 1.12% | 13.01% | NA |
| Indica I | 595 | 30.90% | 24.70% | 1.68% | 42.69% | NA |
| Indica II | 465 | 20.20% | 2.40% | 3.44% | 73.98% | NA |
| Indica III | 913 | 23.80% | 40.10% | 1.86% | 34.28% | NA |
| Indica Intermediate | 786 | 26.00% | 19.50% | 2.67% | 51.91% | NA |
| Temperate Japonica | 767 | 97.00% | 0.30% | 0.13% | 2.61% | NA |
| Tropical Japonica | 504 | 99.20% | 0.60% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.80% | 0.41% | 2.49% | NA |
| VI/Aromatic | 96 | 5.20% | 8.30% | 6.25% | 80.21% | NA |
| Intermediate | 90 | 58.90% | 18.90% | 5.56% | 16.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0801342227 | G -> T | LOC_Os08g03020.1 | missense_variant ; p.Ala357Glu; MODERATE | nonsynonymous_codon ; A357E | Average:7.576; most accessible tissue: Callus, score: 25.686 | benign  |
0.355 |
TOLERATED | 1.00 |
| vg0801342227 | G -> DEL | LOC_Os08g03020.1 | N | frameshift_variant | Average:7.576; most accessible tissue: Callus, score: 25.686 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0801342227 | NA | 2.04E-09 | mr1162 | 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 |
| vg0801342227 | NA | 1.38E-11 | mr1277 | 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 |
| vg0801342227 | NA | 2.21E-06 | mr1577 | 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 |
| vg0801342227 | NA | 3.81E-07 | mr1587 | 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 |
| vg0801342227 | NA | 5.00E-08 | mr1803 | 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 |