Search for Variation information by Variation ID:
Detailed information for vg0413452048:
| Variant ID: vg0413452048 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 13452048 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.19, others allele: 0.00, population size: 163. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTTCAGGAACAAGGGGAATGCTAGAATGATGCGTTGGCACGCTGAAGAACGTCAACAGGACGGAATGCTGAGACACCCCGCAGATGGTTCGCAGTGGC[A/G]
AAACATCGACAGAAAATTTAAAGACTTTGGAAAGGACGCACGAAACATACGGTTTGGTTTAAGTACGGATGGCATGAATCCTTTTGGAGAGATGAGCAGC
Reverse complement sequence
GCTGCTCATCTCTCCAAAAGGATTCATGCCATCCGTACTTAAACCAAACCGTATGTTTCGTGCGTCCTTTCCAAAGTCTTTAAATTTTCTGTCGATGTTT[T/C]
GCCACTGCGAACCATCTGCGGGGTGTCTCAGCATTCCGTCCTGTTGACGTTCTTCAGCGTGCCAACGCATCATTCTAGCATTCCCCTTGTTCCTGAACAA
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 | 86.20% | 0.10% | 5.80% | 7.87% | NA |
| All Indica | 2759 | 80.10% | 0.10% | 9.64% | 10.18% | NA |
| All Japonica | 1512 | 99.60% | 0.10% | 0.20% | 0.13% | NA |
| Aus | 269 | 68.40% | 0.00% | 0.37% | 31.23% | NA |
| Indica I | 595 | 81.20% | 0.20% | 10.92% | 7.73% | NA |
| Indica II | 465 | 81.10% | 0.20% | 14.41% | 4.30% | NA |
| Indica III | 913 | 81.60% | 0.00% | 6.79% | 11.61% | NA |
| Indica Intermediate | 786 | 76.80% | 0.10% | 9.16% | 13.87% | NA |
| Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.20% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 3.10% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 3.33% | 3.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0413452048 | A -> DEL | LOC_Os04g23520.1 | N | frameshift_variant | Average:9.651; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0413452048 | A -> G | LOC_Os04g23520.1 | missense_variant ; p.Gln318Arg; MODERATE | nonsynonymous_codon ; Q318R | Average:9.651; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
-0.798 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0413452048 | 8.09E-06 | NA | mr1697 | 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 |