Search for Variation information by Variation ID:
Detailed information for vg0307860069:
| Variant ID: vg0307860069 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 7860069 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
AAGACATACGAAGCAAAGCATGTTCTGTGTCCACTGGGGTTAGAGGTCCGTAGAATTCACGCTTGTCCAAACGACTGCATATTGTACCACAAGCAATATG[C/T]
GGACTTGGATGCTTGTCCTGTCTGCAAGGCTTCTCGATACAAGTGAAAGAAAAGTGCTGACGAAGGAAAGAAGTCAAAGAGGGGTGGTCCGGCAAAGGTT
Reverse complement sequence
AACCTTTGCCGGACCACCCCTCTTTGACTTCTTTCCTTCGTCAGCACTTTTCTTTCACTTGTATCGAGAAGCCTTGCAGACAGGACAAGCATCCAAGTCC[G/A]
CATATTGCTTGTGGTACAATATGCAGTCGTTTGGACAAGCGTGAATTCTACGGACCTCTAACCCCAGTGGACACAGAACATGCTTTGCTTCGTATGTCTT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 67.90% | 3.30% | 14.68% | 14.18% | NA |
| All Indica | 2759 | 54.00% | 4.80% | 17.69% | 23.49% | NA |
| All Japonica | 1512 | 86.70% | 1.20% | 11.18% | 0.93% | NA |
| Aus | 269 | 96.70% | 0.40% | 2.97% | 0.00% | NA |
| Indica I | 595 | 49.60% | 0.00% | 15.97% | 34.45% | NA |
| Indica II | 465 | 23.90% | 10.80% | 15.91% | 49.46% | NA |
| Indica III | 913 | 69.10% | 4.60% | 20.37% | 5.91% | NA |
| Indica Intermediate | 786 | 57.60% | 5.20% | 16.92% | 20.23% | NA |
| Temperate Japonica | 767 | 98.20% | 0.10% | 1.30% | 0.39% | NA |
| Tropical Japonica | 504 | 66.10% | 3.00% | 29.17% | 1.79% | NA |
| Japonica Intermediate | 241 | 93.40% | 0.80% | 4.98% | 0.83% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 8.33% | 0.00% | NA |
| Intermediate | 90 | 65.60% | 2.20% | 23.33% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0307860069 | C -> T | LOC_Os03g14460.1 | missense_variant ; p.Ala187Val; MODERATE | nonsynonymous_codon ; A187V | Average:29.007; most accessible tissue: Minghui63 young leaf, score: 40.718 | benign  |
0.425 |
TOLERATED | 0.05 |
| vg0307860069 | C -> DEL | LOC_Os03g14460.1 | N | frameshift_variant | Average:29.007; most accessible tissue: Minghui63 young leaf, score: 40.718 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0307860069 | 1.77E-06 | 4.50E-06 | mr1401 | Ind_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 |