Search for Variation information by Variation ID:
Detailed information for vg0229172293:
| Variant ID: vg0229172293 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 29172293 |
| 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, others allele: 0.00, population size: 259. )
Flanking Sequence (100 bp) in Reference Genome:
TCAACTCTAATGATGGATCGACTGCTTAACCTCCAAGGACCTCCCTTAGGCAGTATCGACAATATTGAGTTTGCAGGATTCAGGAGCAGGAACTTTGACA[G/A]
ATGGTGGGGTGAATGGAAGTTGCATCTATTTCATCAATCGGCCACAATGTACATGACAGATCTATTCCCTGACGTCATACCCCAGGTAAACTTTGTCATC
Reverse complement sequence
GATGACAAAGTTTACCTGGGGTATGACGTCAGGGAATAGATCTGTCATGTACATTGTGGCCGATTGATGAAATAGATGCAACTTCCATTCACCCCACCAT[C/T]
TGTCAAAGTTCCTGCTCCTGAATCCTGCAAACTCAATATTGTCGATACTGCCTAAGGGAGGTCCTTGGAGGTTAAGCAGTCGATCCATCATTAGAGTTGA
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 | 84.40% | 15.20% | 0.34% | 0.04% | NA |
| All Indica | 2759 | 96.20% | 3.60% | 0.18% | 0.07% | NA |
| All Japonica | 1512 | 74.30% | 25.10% | 0.66% | 0.00% | NA |
| Aus | 269 | 16.40% | 83.30% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica II | 465 | 97.20% | 2.20% | 0.43% | 0.22% | NA |
| Indica III | 913 | 96.90% | 3.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 92.20% | 7.40% | 0.25% | 0.13% | NA |
| Temperate Japonica | 767 | 94.90% | 4.40% | 0.65% | 0.00% | NA |
| Tropical Japonica | 504 | 49.80% | 49.40% | 0.79% | 0.00% | NA |
| Japonica Intermediate | 241 | 59.80% | 39.80% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 83.30% | 16.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0229172293 | G -> A | LOC_Os02g47720.1 | missense_variant ; p.Arg449Lys; MODERATE | nonsynonymous_codon ; R449K | Average:13.573; most accessible tissue: Minghui63 panicle, score: 25.313 | benign  |
0.575 |
DELETERIOUS | 0.04 |
| vg0229172293 | G -> DEL | LOC_Os02g47720.1 | N | frameshift_variant | Average:13.573; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0229172293 | 4.45E-06 | NA | mr1136 | 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 |
| vg0229172293 | NA | 2.43E-07 | mr1180 | 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 |
| vg0229172293 | NA | 5.39E-07 | mr1183 | 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 |
| vg0229172293 | NA | 1.42E-06 | mr1503 | 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 |
| vg0229172293 | NA | 3.74E-07 | mr1180_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 |