Search for Variation information by Variation ID:
Detailed information for vg0608868763:
| Variant ID: vg0608868763 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8868763 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCATCTCCCGCGAAAACCGCCGCGACTCCTCCGTAGCGCTTGCTTCGGCCTTGCGAACCTCCTGCCGAAGAGCCTCCATCTTCGGCTCGGTGAGGTTGTA[A/G]
TAATCTATGAGCACGGCGGAGTGGGCCTTCTCTTTCTCCAGTTCGGCCTTTAAGAGATCGACTTCGGCCCTAGCTTCCTTCCCTTTCTCCCGTTCCGATT
Reverse complement sequence
AATCGGAACGGGAGAAAGGGAAGGAAGCTAGGGCCGAAGTCGATCTCTTAAAGGCCGAACTGGAGAAAGAGAAGGCCCACTCCGCCGTGCTCATAGATTA[T/C]
TACAACCTCACCGAGCCGAAGATGGAGGCTCTTCGGCAGGAGGTTCGCAAGGCCGAAGCAAGCGCTACGGAGGAGTCGCGGCGGTTTTCGCGGGAGATGG
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 | 89.70% | 5.10% | 0.78% | 4.46% | NA |
| All Indica | 2759 | 99.50% | 0.30% | 0.07% | 0.14% | NA |
| All Japonica | 1512 | 70.00% | 14.50% | 2.18% | 13.29% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.17% | 0.17% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.50% | 0.40% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.20% | 0.40% | 0.00% | 0.38% | NA |
| Temperate Japonica | 767 | 82.80% | 3.50% | 1.04% | 12.65% | NA |
| Tropical Japonica | 504 | 60.50% | 30.80% | 2.78% | 5.95% | NA |
| Japonica Intermediate | 241 | 49.40% | 15.40% | 4.56% | 30.71% | NA |
| VI/Aromatic | 96 | 85.40% | 11.50% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 92.20% | 2.20% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0608868763 | A -> G | LOC_Os06g15660.1 | synonymous_variant ; p.Tyr94Tyr; LOW | synonymous_codon | Average:28.412; most accessible tissue: Callus, score: 43.705 | N | N | N | N |
| vg0608868763 | A -> G | LOC_Os06g15660.1 | synonymous_variant ; p.Tyr94Tyr; LOW | nonsynonymous_codon ; Y94H | Average:28.412; most accessible tissue: Callus, score: 43.705 | probably damaging  |
2.025 |
DELETERIOUS | 0.00 |
| vg0608868763 | A -> DEL | LOC_Os06g15660.1 | N | frameshift_variant | Average:28.412; most accessible tissue: Callus, score: 43.705 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608868763 | 4.58E-06 | NA | mr1976_2 | Jap_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 |