Search for Variation information by Variation ID:
Detailed information for vg0316679196:
| Variant ID: vg0316679196 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 16679196 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 128. )
Flanking Sequence (100 bp) in Reference Genome:
TCGGACATTTTTTTCCTCAAAGCCAAATGCTTCAGCTGTTGTATGATCCGCAACAAATGTATCCCAATCAACCTGCGATATATGTCCATAATCCATGAAC[G/A]
GTGGGAGATTCTTCTGAACATAATCCCGATTTAGATCGGACTTCCACTGTCGCCATCGATCTCCCATCTTTTTAAGTGCGTAATCTCTCCCCCTGACCTC
Reverse complement sequence
GAGGTCAGGGGGAGAGATTACGCACTTAAAAAGATGGGAGATCGATGGCGACAGTGGAAGTCCGATCTAAATCGGGATTATGTTCAGAAGAATCTCCCAC[C/T]
GTTCATGGATTATGGACATATATCGCAGGTTGATTGGGATACATTTGTTGCGGATCATACAACAGCTGAAGCATTTGGCTTTGAGGAAAAAAATGTCCGA
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 | 88.70% | 11.20% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 85.70% | 14.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 92.10% | 7.70% | 0.13% | 0.00% | NA |
| Aus | 269 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
| Indica I | 595 | 64.00% | 36.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 84.50% | 15.30% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 77.40% | 22.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 92.20% | 6.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0316679196 | G -> A | LOC_Os03g29290.1 | missense_variant ; p.Pro219Leu; MODERATE | nonsynonymous_codon ; P219L | Average:42.844; most accessible tissue: Minghui63 flag leaf, score: 62.47 | probably damaging  |
2.204 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0316679196 | NA | 1.03E-06 | mr1633 | 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 |
| vg0316679196 | NA | 2.57E-06 | mr1633 | 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 |
| vg0316679196 | NA | 5.62E-06 | mr1922 | 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 |
| vg0316679196 | NA | 5.78E-06 | mr1567_2 | Jap_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 |
| vg0316679196 | NA | 9.33E-06 | mr1739_2 | Jap_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 |