Search for Variation information by Variation ID:
Detailed information for vg0202539979:
| Variant ID: vg0202539979 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 2539979 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.08, others allele: 0.00, population size: 241. )
Flanking Sequence (100 bp) in Reference Genome:
AGTTTGGTACTTCAAGGTTTCGACGAGATGGGTTCAAAAGATGGATTCTCTGACAACAAGCTATTCGACGACTTCGCTGTGGGAAGATCCAACCCGACCG[A/G]
AGTATGTCTCCCGACGAGATCGGAACCATCGTCATCAACAACTCGATCTCTCGAGATCGACCAAACCTCAAGATACGCGGCGTACCAAAAGACGTCAGAT
Reverse complement sequence
ATCTGACGTCTTTTGGTACGCCGCGTATCTTGAGGTTTGGTCGATCTCGAGAGATCGAGTTGTTGATGACGATGGTTCCGATCTCGTCGGGAGACATACT[T/C]
CGGTCGGGTTGGATCTTCCCACAGCGAAGTCGTCGAATAGCTTGTTGTCAGAGAATCCATCTTTTGAACCCATCTCGTCGAAACCTTGAAGTACCAAACT
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 | 80.90% | 19.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 43.40% | 56.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 8.60% | 91.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 90.10% | 9.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 56.40% | 43.60% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 74.40% | 25.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0202539979 | A -> G | LOC_Os02g05290.1 | missense_variant ; p.Glu25Gly; MODERATE | nonsynonymous_codon ; E25G | Average:46.714; most accessible tissue: Minghui63 young leaf, score: 61.887 | benign  |
-0.233 |
TOLERATED | 0.37 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0202539979 | NA | 1.34E-21 | mr1300 | 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 |
| vg0202539979 | NA | 6.78E-11 | mr1712 | 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 |
| vg0202539979 | NA | 1.77E-06 | mr1826 | 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 |