Search for Variation information by Variation ID:
Detailed information for vg0315800734:
| Variant ID: vg0315800734 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15800734 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCGGTGTGTTGCAGTCTCGCTTTAACATCGTTTGTCGTCTAGCTCGGATGTGGAGGCAGGGCGATGTTATCAATATAATGGAAGCTTGTGTTATTCTTC[G/A]
CAATATGATAGTTGAAGATGAACAGGAAATGGCTGAAATTCCTTTGGATTTAAATGAGAACCCAGGAGCATCGTTCGTTCTACCACCTGAAGTGAGGAAC
Reverse complement sequence
GTTCCTCACTTCAGGTGGTAGAACGAACGATGCTCCTGGGTTCTCATTTAAATCCAAAGGAATTTCAGCCATTTCCTGTTCATCTTCAACTATCATATTG[C/T]
GAAGAATAACACAAGCTTCCATTATATTGATAACATCGCCCTGCCTCCACATCCGAGCTAGACGACAAACGATGTTAAAGCGAGACTGCAACACACCGAA
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 | 29.90% | 4.40% | 0.85% | 64.94% | NA |
| All Indica | 2759 | 11.40% | 0.70% | 0.80% | 87.10% | NA |
| All Japonica | 1512 | 63.30% | 2.60% | 1.12% | 33.00% | NA |
| Aus | 269 | 16.00% | 48.30% | 0.00% | 35.69% | NA |
| Indica I | 595 | 3.70% | 0.00% | 1.68% | 94.62% | NA |
| Indica II | 465 | 13.10% | 0.00% | 0.86% | 86.02% | NA |
| Indica III | 913 | 18.50% | 1.30% | 0.00% | 80.18% | NA |
| Indica Intermediate | 786 | 7.90% | 1.00% | 1.02% | 90.08% | NA |
| Temperate Japonica | 767 | 89.20% | 4.30% | 1.96% | 4.56% | NA |
| Tropical Japonica | 504 | 21.80% | 0.00% | 0.20% | 77.98% | NA |
| Japonica Intermediate | 241 | 67.60% | 2.50% | 0.41% | 29.46% | NA |
| VI/Aromatic | 96 | 76.00% | 6.20% | 0.00% | 17.71% | NA |
| Intermediate | 90 | 26.70% | 12.20% | 1.11% | 60.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0315800734 | G -> A | LOC_Os03g27540.1 | missense_variant ; p.Arg551His; MODERATE | nonsynonymous_codon ; R551H | Average:28.316; most accessible tissue: Zhenshan97 young leaf, score: 50.669 | possibly damaging  |
-1.538 |
TOLERATED | 1.00 |
| vg0315800734 | G -> DEL | LOC_Os03g27540.1 | N | frameshift_variant | Average:28.316; most accessible tissue: Zhenshan97 young leaf, score: 50.669 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0315800734 | NA | 1.91E-06 | mr1603_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 |
| vg0315800734 | NA | 7.47E-08 | mr1612_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 |
| vg0315800734 | 7.43E-07 | NA | mr1940_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 |