Search for Variation information by Variation ID:
Detailed information for vg0200521736:
| Variant ID: vg0200521736 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 521736 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 128. )
Flanking Sequence (100 bp) in Reference Genome:
TTCGATTTGGGTTATATCGAGGATAGATTTAGATCACAATCATGAGCTCAGTCCTCCAGATGAGGCTAGATTTCTAAGATCTCACAAATACATGTCGACA[G/A]
AAGAAAAGATTCTAATCAGGACTTTGAAAGAATGCCATATTCCAACAAGAAATATGATTGTAATATTATCTGTTCTAAGAGGTGGTCTAACTTCTTTGCC
Reverse complement sequence
GGCAAAGAAGTTAGACCACCTCTTAGAACAGATAATATTACAATCATATTTCTTGTTGGAATATGGCATTCTTTCAAAGTCCTGATTAGAATCTTTTCTT[C/T]
TGTCGACATGTATTTGTGAGATCTTAGAAATCTAGCCTCATCTGGAGGACTGAGCTCATGATTGTGATCTAAATCTATCCTCGATATAACCCAAATCGAA
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 | 96.00% | 0.90% | 1.04% | 2.05% | NA |
| All Indica | 2759 | 93.20% | 1.50% | 1.78% | 3.48% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 77.30% | 4.70% | 6.55% | 11.43% | NA |
| Indica II | 465 | 95.90% | 1.10% | 0.65% | 2.37% | NA |
| Indica III | 913 | 99.80% | 0.10% | 0.00% | 0.11% | NA |
| Indica Intermediate | 786 | 96.10% | 1.00% | 0.89% | 2.04% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 0.00% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0200521736 | G -> A | LOC_Os02g01950.1 | missense_variant ; p.Glu216Lys; MODERATE | nonsynonymous_codon ; E216K | Average:18.896; most accessible tissue: Zhenshan97 root, score: 29.203 | benign  |
1.487 |
TOLERATED | 0.11 |
| vg0200521736 | G -> DEL | LOC_Os02g01950.1 | N | frameshift_variant | Average:18.896; most accessible tissue: Zhenshan97 root, score: 29.203 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0200521736 | 5.03E-06 | NA | mr1245_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 |
| vg0200521736 | 8.33E-08 | 4.33E-07 | mr1373_2 | 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 |
| vg0200521736 | 3.68E-06 | 3.77E-06 | mr1373_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 |
| vg0200521736 | NA | 9.51E-06 | mr1417_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 |