Search for Variation information by Variation ID:
Detailed information for vg0420807529:
| Variant ID: vg0420807529 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20807529 |
| Reference Allele: A | Alternative Allele: T,G |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, others allele: 0.00, population size: 88. )
Flanking Sequence (100 bp) in Reference Genome:
CCAGCGAGAGAAAGACCAGAAACAAAGTAATCAGATTCTGCAAGGTTCAGTGGAGTCATCACTCAGAAGAAGAGGCCACTTGGGAAAGAGAAGATGAGTT[A/T,G]
AAGGCCACCCACCCGCACCTCTTCGCCAGCTCTTCCGAATCTCGAGGTCGAGATTCCGTTTAAGGGGGGTAGGTTTGTCACACCCTGAAGTTTCCCCCCT
Reverse complement sequence
AGGGGGGAAACTTCAGGGTGTGACAAACCTACCCCCCTTAAACGGAATCTCGACCTCGAGATTCGGAAGAGCTGGCGAAGAGGTGCGGGTGGGTGGCCTT[T/A,C]
AACTCATCTTCTCTTTCCCAAGTGGCCTCTTCTTCTGAGTGATGACTCCACTGAACCTTGCAGAATCTGATTACTTTGTTTCTGGTCTTTCTCTCGCTGG
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 24.10% | 0.90% | 3.09% | 71.82% | G: 0.08% |
| All Indica | 2759 | 3.00% | 1.50% | 4.17% | 91.26% | G: 0.11% |
| All Japonica | 1512 | 64.50% | 0.00% | 0.13% | 35.38% | NA |
| Aus | 269 | 1.90% | 0.00% | 9.67% | 88.10% | G: 0.37% |
| Indica I | 595 | 2.90% | 1.00% | 1.51% | 94.62% | NA |
| Indica II | 465 | 3.70% | 1.50% | 2.15% | 92.47% | G: 0.22% |
| Indica III | 913 | 1.30% | 1.30% | 7.45% | 89.92% | NA |
| Indica Intermediate | 786 | 4.60% | 2.00% | 3.56% | 89.57% | G: 0.25% |
| Temperate Japonica | 767 | 82.30% | 0.00% | 0.13% | 17.60% | NA |
| Tropical Japonica | 504 | 36.30% | 0.00% | 0.20% | 63.49% | NA |
| Japonica Intermediate | 241 | 66.80% | 0.00% | 0.00% | 33.20% | NA |
| VI/Aromatic | 96 | 43.80% | 0.00% | 1.04% | 55.21% | NA |
| Intermediate | 90 | 40.00% | 1.10% | 2.22% | 56.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420807529 | A -> DEL | LOC_Os04g34350.1 | N | frameshift_variant | Average:14.37; most accessible tissue: Callus, score: 23.793 | N | N | N | N |
| vg0420807529 | A -> G | LOC_Os04g34350.1 | synonymous_variant ; p.Leu1442Leu; LOW | synonymous_codon | Average:14.37; most accessible tissue: Callus, score: 23.793 | N | N | N | N |
| vg0420807529 | A -> T | LOC_Os04g34350.1 | missense_variant ; p.Leu1442Phe; MODERATE | nonsynonymous_codon ; L1442C | Average:14.37; most accessible tissue: Callus, score: 23.793 | probably damaging  |
2.629 |
DELETERIOUS | 0.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0420807529 | NA | 2.43E-08 | mr1248 | Jap_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 |
| vg0420807529 | 4.76E-06 | NA | mr1486_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 |
| vg0420807529 | 3.73E-07 | NA | mr1486_2 | 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 |