Search for Variation information by Variation ID:
Detailed information for vg0100911990:
| Variant ID: vg0100911990 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 911990 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CTCTTCTGAAATTGCAGTAAGCTCGGAGGAGTGAAAGTAAGAATCCATGACTTGTGGAGGTGGCATGCCATTGCCAATGCCATCCCCATCGCAGAAAAAT[G/A]
GTCTCGGAGGCACTTGCAGCGCATCCACACCCCCTTCGAGCATCTCTATTGCCTCGCTCATCGTCAGGCGATCGTGTGATTTCATCTGAATGCACCACAG
Reverse complement sequence
CTGTGGTGCATTCAGATGAAATCACACGATCGCCTGACGATGAGCGAGGCAATAGAGATGCTCGAAGGGGGTGTGGATGCGCTGCAAGTGCCTCCGAGAC[C/T]
ATTTTTCTGCGATGGGGATGGCATTGGCAATGGCATGCCACCTCCACAAGTCATGGATTCTTACTTTCACTCCTCCGAGCTTACTGCAATTTCAGAAGAG
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 | 99.20% | 0.20% | 0.47% | 0.17% | NA |
| All Indica | 2759 | 99.70% | 0.10% | 0.18% | 0.04% | NA |
| All Japonica | 1512 | 98.30% | 0.30% | 1.06% | 0.40% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.20% | 0.30% | 0.34% | 0.17% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.00% | 0.60% | 3.17% | 1.19% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0100911990 | G -> A | LOC_Os01g02680.1 | missense_variant ; p.Pro667Leu; MODERATE | nonsynonymous_codon ; P667L | Average:25.613; most accessible tissue: Callus, score: 41.359 | probably damaging  |
2.029 |
DELETERIOUS | 0.00 |
| vg0100911990 | G -> DEL | LOC_Os01g02680.1 | N | frameshift_variant | Average:25.613; most accessible tissue: Callus, score: 41.359 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0100911990 | 7.45E-07 | NA | mr1925 | Jap_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 |