Search for Variation information by Variation ID:
Detailed information for vg0808455943:
| Variant ID: vg0808455943 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 8455943 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 227. )
Flanking Sequence (100 bp) in Reference Genome:
GTAGTCGACAACAGGGTAGCCTTCCTCCTCAAATCCGTGTTCGGCAAGATCAGAGATAGCGCTTTCGTATCTCCTGACGGTATCCGGAGACACCGTAGGG[G/A]
AATAGCCATGCCTATCCCTGAAGTCGATATCCGGCAGCGTGTCTTGGCGTATGTAGGCTTGTGTGTTGTGGCTTCTGGTGGGCGTGTGTTGATTGTCATG
Reverse complement sequence
CATGACAATCAACACACGCCCACCAGAAGCCACAACACACAAGCCTACATACGCCAAGACACGCTGCCGGATATCGACTTCAGGGATAGGCATGGCTATT[C/T]
CCCTACGGTGTCTCCGGATACCGTCAGGAGATACGAAAGCGCTATCTCTGATCTTGCCGAACACGGATTTGAGGAGGAAGGCTACCCTGTTGTCGACTAC
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 | 93.60% | 3.20% | 2.20% | 0.95% | NA |
| All Indica | 2759 | 99.80% | 0.00% | 0.18% | 0.04% | NA |
| All Japonica | 1512 | 81.40% | 9.90% | 5.82% | 2.91% | NA |
| Aus | 269 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Temperate Japonica | 767 | 83.40% | 11.50% | 3.52% | 1.56% | NA |
| Tropical Japonica | 504 | 88.70% | 1.40% | 7.14% | 2.78% | NA |
| Japonica Intermediate | 241 | 59.80% | 22.40% | 10.37% | 7.47% | NA |
| VI/Aromatic | 96 | 91.70% | 1.00% | 7.29% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 0.00% | 4.44% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0808455943 | G -> A | LOC_Os08g14160.1 | missense_variant ; p.Ser38Phe; MODERATE | nonsynonymous_codon ; S38F | Average:11.409; most accessible tissue: Callus, score: 26.865 | probably damaging  |
2.23 |
TOLERATED | 0.07 |
| vg0808455943 | G -> DEL | LOC_Os08g14160.1 | N | frameshift_variant | Average:11.409; most accessible tissue: Callus, score: 26.865 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0808455943 | 8.71E-07 | NA | mr1172_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 |