Search for Variation information by Variation ID:
Detailed information for vg1218662517:
| Variant ID: vg1218662517 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18662517 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCAACTCCCCTACCTCGGCAGCCGTCTCTTGCTCCTCAGTCGTATCTTGCTCCACCCCTTGACGAACGTGTGCCACCTCCCCAGCCAGATACATCAAAGG[A/G]
GCAGCCAAATACCTGTGAAGCTCGGAAGCTCATACTTGTTATGGTTTCCACGTACAACAAGGAGAAAATGGCAGAGTATGAGACGCGGATGGTTTTGCAG
Reverse complement sequence
CTGCAAAACCATCCGCGTCTCATACTCTGCCATTTTCTCCTTGTTGTACGTGGAAACCATAACAAGTATGAGCTTCCGAGCTTCACAGGTATTTGGCTGC[T/C]
CCTTTGATGTATCTGGCTGGGGAGGTGGCACACGTTCGTCAAGGGGTGGAGCAAGATACGACTGAGGAGCAAGAGACGGCTGCCGAGGTAGGGGAGTTGG
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 | 46.40% | 3.30% | 35.08% | 15.19% | NA |
| All Indica | 2759 | 38.80% | 4.60% | 47.59% | 8.99% | NA |
| All Japonica | 1512 | 57.40% | 1.20% | 11.64% | 29.76% | NA |
| Aus | 269 | 66.50% | 2.20% | 31.23% | 0.00% | NA |
| Indica I | 595 | 27.10% | 3.00% | 49.08% | 20.84% | NA |
| Indica II | 465 | 29.70% | 3.90% | 54.41% | 12.04% | NA |
| Indica III | 913 | 50.10% | 6.10% | 42.28% | 1.53% | NA |
| Indica Intermediate | 786 | 40.10% | 4.50% | 48.60% | 6.87% | NA |
| Temperate Japonica | 767 | 64.80% | 0.10% | 4.82% | 30.25% | NA |
| Tropical Japonica | 504 | 54.20% | 2.60% | 24.60% | 18.65% | NA |
| Japonica Intermediate | 241 | 40.70% | 1.70% | 6.22% | 51.45% | NA |
| VI/Aromatic | 96 | 20.80% | 6.20% | 59.38% | 13.54% | NA |
| Intermediate | 90 | 60.00% | 1.10% | 31.11% | 7.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218662517 | A -> DEL | LOC_Os12g31050.1 | N | frameshift_variant | Average:24.225; most accessible tissue: Callus, score: 51.178 | N | N | N | N |
| vg1218662517 | A -> G | LOC_Os12g31050.1 | missense_variant ; p.Glu518Gly; MODERATE | nonsynonymous_codon ; E518G | Average:24.225; most accessible tissue: Callus, score: 51.178 | benign  |
1.064 |
TOLERATED | 0.07 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1218662517 | 2.86E-06 | 7.51E-07 | mr1702 | 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 |