Search for Variation information by Variation ID:
Detailed information for vg0713784416:
| Variant ID: vg0713784416 (JBrowse) | Variation Type: SNP |
| Chromosome: chr07 | Position: 13784416 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 96. )
Flanking Sequence (100 bp) in Reference Genome:
CTTGGGAAAGAACTTCAGGGTGTGACAAACCTACCCCCCTTAAACGGAATCTCGGCCCCGAGATTCGGAAGAGCTGGTGAAGAGGTGCGGATGGGCGGCC[T/A]
TTAGCTCATCTTCCCTTTCCCGGGTTGCTTCTTCGTCTGAGTGGTGGCTCCACTGAACCCTGCAGAACCTGGTGACCTTATTCCTAGTCCTCCTTTCACT
Reverse complement sequence
AGTGAAAGGAGGACTAGGAATAAGGTCACCAGGTTCTGCAGGGTTCAGTGGAGCCACCACTCAGACGAAGAAGCAACCCGGGAAAGGGAAGATGAGCTAA[A/T]
GGCCGCCCATCCGCACCTCTTCACCAGCTCTTCCGAATCTCGGGGCCGAGATTCCGTTTAAGGGGGGTAGGTTTGTCACACCCTGAAGTTCTTTCCCAAG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.90% | 3.40% | 3.91% | 13.82% | NA |
| All Indica | 2759 | 80.90% | 5.50% | 4.46% | 9.17% | NA |
| All Japonica | 1512 | 73.20% | 0.00% | 2.05% | 24.74% | NA |
| Aus | 269 | 82.90% | 1.90% | 7.43% | 7.81% | NA |
| Indica I | 595 | 58.80% | 16.30% | 8.24% | 16.64% | NA |
| Indica II | 465 | 93.10% | 0.60% | 1.51% | 4.73% | NA |
| Indica III | 913 | 95.00% | 0.00% | 3.94% | 1.10% | NA |
| Indica Intermediate | 786 | 73.90% | 6.60% | 3.94% | 15.52% | NA |
| Temperate Japonica | 767 | 66.10% | 0.00% | 2.61% | 31.29% | NA |
| Tropical Japonica | 504 | 94.60% | 0.00% | 2.18% | 3.17% | NA |
| Japonica Intermediate | 241 | 51.00% | 0.00% | 0.00% | 48.96% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 6.25% | 1.04% | NA |
| Intermediate | 90 | 87.80% | 2.20% | 5.56% | 4.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0713784416 | T -> DEL | LOC_Os07g24240.1 | N | frameshift_variant | Average:38.088; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 | N | N | N | N |
| vg0713784416 | T -> A | LOC_Os07g24240.1 | missense_variant ; p.Lys510Met; MODERATE | nonsynonymous_codon ; K510M | Average:38.088; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 | probably damaging  |
2.746 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0713784416 | 1.13E-07 | NA | mr1235 | 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 |
| vg0713784416 | 1.54E-07 | NA | mr1235 | 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 |