Search for Variation information by Variation ID:
Detailed information for vg0818860176:
| Variant ID: vg0818860176 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 18860176 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.69, A: 0.31, others allele: 0.00, population size: 78. )
Flanking Sequence (100 bp) in Reference Genome:
CCACAGCATCTCTTTCTCCGAATCTGGGACAAAGCTCTCATGATCTCCGCGTGCCCTTGTTCTGCGCCAGTAGACCGTACTAACAGGCACGTTATCCCGC[G/A]
CAACCCAACCGCTGTGACGTACATAGTTCTTGGCGGCTTCTGCCGGGGCACTAGGTCGGCCGTCTTCGTCCACTTCCGTTATGATGTGCCGACCCTCAAG
Reverse complement sequence
CTTGAGGGTCGGCACATCATAACGGAAGTGGACGAAGACGGCCGACCTAGTGCCCCGGCAGAAGCCGCCAAGAACTATGTACGTCACAGCGGTTGGGTTG[C/T]
GCGGGATAACGTGCCTGTTAGTACGGTCTACTGGCGCAGAACAAGGGCACGCGGAGATCATGAGAGCTTTGTCCCAGATTCGGAGAAAGAGATGCTGTGG
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 | 36.70% | 31.50% | 29.20% | 2.58% | NA |
| All Indica | 2759 | 8.90% | 50.10% | 37.77% | 3.19% | NA |
| All Japonica | 1512 | 86.70% | 2.10% | 11.18% | 0.00% | NA |
| Aus | 269 | 14.90% | 17.10% | 56.51% | 11.52% | NA |
| Indica I | 595 | 18.70% | 37.60% | 36.97% | 6.72% | NA |
| Indica II | 465 | 6.20% | 41.10% | 49.03% | 3.66% | NA |
| Indica III | 913 | 5.00% | 68.50% | 26.29% | 0.22% | NA |
| Indica Intermediate | 786 | 7.60% | 43.60% | 45.04% | 3.69% | NA |
| Temperate Japonica | 767 | 99.50% | 0.10% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 64.90% | 5.60% | 29.56% | 0.00% | NA |
| Japonica Intermediate | 241 | 91.70% | 1.20% | 7.05% | 0.00% | NA |
| VI/Aromatic | 96 | 88.50% | 5.20% | 4.17% | 2.08% | NA |
| Intermediate | 90 | 57.80% | 26.70% | 14.44% | 1.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0818860176 | G -> A | LOC_Os08g30600.1 | missense_variant ; p.Ala120Val; MODERATE | nonsynonymous_codon ; A120V | Average:29.268; most accessible tissue: Zhenshan97 root, score: 58.674 | benign  |
-1.284 |
TOLERATED | 1.00 |
| vg0818860176 | G -> DEL | LOC_Os08g30600.1 | N | frameshift_variant | Average:29.268; most accessible tissue: Zhenshan97 root, score: 58.674 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0818860176 | NA | 5.77E-06 | mr1639 | 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 |
| vg0818860176 | NA | 4.30E-08 | mr1047_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 |
| vg0818860176 | NA | 3.26E-06 | mr1389_2 | Ind_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 |
| vg0818860176 | NA | 1.54E-06 | mr1754_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 |