Search for Variation information by Variation ID:
Detailed information for vg1121817225:
| Variant ID: vg1121817225 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 21817225 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, A: 0.38, others allele: 0.00, population size: 74. )
Flanking Sequence (100 bp) in Reference Genome:
ATGCAGGGAAATTATTTTCCCTGCCCATTTGGAATTTGTCTTCTGTTTATTGTTACTGAAATTAGCTTTTTTTTATCAATGGAAGATCCAAGCATCCACC[G/A]
ATGAGGCACCTCATAGACGAAAAGAAGCACTTGGGAAGAAGAGCTCCGCTGCAAAAGCTATAGGTTCTTCAAGGTCTCAAGGGAATATGCTGGCAAGGAA
Reverse complement sequence
TTCCTTGCCAGCATATTCCCTTGAGACCTTGAAGAACCTATAGCTTTTGCAGCGGAGCTCTTCTTCCCAAGTGCTTCTTTTCGTCTATGAGGTGCCTCAT[C/T]
GGTGGATGCTTGGATCTTCCATTGATAAAAAAAAGCTAATTTCAGTAACAATAAACAGAAGACAAATTCCAAATGGGCAGGGAAAATAATTTCCCTGCAT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 26.60% | 17.20% | 0.57% | 55.63% | NA |
| All Indica | 2759 | 28.60% | 1.40% | 0.76% | 69.19% | NA |
| All Japonica | 1512 | 20.90% | 49.30% | 0.20% | 29.56% | NA |
| Aus | 269 | 20.80% | 3.70% | 0.74% | 74.72% | NA |
| Indica I | 595 | 23.00% | 1.50% | 0.17% | 75.29% | NA |
| Indica II | 465 | 31.80% | 1.50% | 1.29% | 65.38% | NA |
| Indica III | 913 | 30.10% | 0.90% | 0.55% | 68.46% | NA |
| Indica Intermediate | 786 | 29.10% | 2.00% | 1.15% | 67.68% | NA |
| Temperate Japonica | 767 | 6.30% | 73.80% | 0.13% | 19.82% | NA |
| Tropical Japonica | 504 | 46.80% | 13.10% | 0.20% | 39.88% | NA |
| Japonica Intermediate | 241 | 13.30% | 47.30% | 0.41% | 39.00% | NA |
| VI/Aromatic | 96 | 72.90% | 0.00% | 0.00% | 27.08% | NA |
| Intermediate | 90 | 30.00% | 17.80% | 1.11% | 51.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1121817225 | G -> A | LOC_Os11g36970.1 | missense_variant ; p.Asp122Asn; MODERATE | nonsynonymous_codon ; D122N | Average:16.64; most accessible tissue: Callus, score: 69.79 | benign  |
1.329 |
TOLERATED | 0.39 |
| vg1121817225 | G -> DEL | LOC_Os11g36970.1 | N | frameshift_variant | Average:16.64; most accessible tissue: Callus, score: 69.79 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1121817225 | NA | 7.03E-06 | mr1865 | 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 |
| vg1121817225 | NA | 6.52E-11 | mr1510_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 |
| vg1121817225 | NA | 1.55E-06 | mr1510_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 |
| vg1121817225 | NA | 2.87E-10 | mr1702_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 |
| vg1121817225 | NA | 4.79E-06 | mr1740_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 |