Variant ID: vg0808162481 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 8162481 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GGTGAGTGTCCCTGGGGTGGCGATGGAATAGAATCAAATCGAGCTAATAAACAGGTCGTGTTGTCTCAGAATGGGCGATATGGTACAAAACTTATTACCG[G/C]
ATGGATTCAGTCGGAGCCAAAGAACAGCGCGCAGAGCGACCTAGGGCTAGGAGTAGAGCTGCGTGGCGTACCTGCTCTCCACCCCACGTCGACGGCGCCG
CGGCGCCGTCGACGTGGGGTGGAGAGCAGGTACGCCACGCAGCTCTACTCCTAGCCCTAGGTCGCTCTGCGCGCTGTTCTTTGGCTCCGACTGAATCCAT[C/G]
CGGTAATAAGTTTTGTACCATATCGCCCATTCTGAGACAACACGACCTGTTTATTAGCTCGATTTGATTCTATTCCATCGCCACCCCAGGGACACTCACC
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 89.80% | 7.70% | 0.42% | 2.05% | NA |
All Indica | 2759 | 95.70% | 0.50% | 0.43% | 3.30% | NA |
All Japonica | 1512 | 86.00% | 13.60% | 0.20% | 0.13% | NA |
Aus | 269 | 51.70% | 46.10% | 0.74% | 1.49% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 82.60% | 0.00% | 1.72% | 15.70% | NA |
Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 95.70% | 1.50% | 0.51% | 2.29% | NA |
Temperate Japonica | 767 | 95.70% | 3.90% | 0.39% | 0.00% | NA |
Tropical Japonica | 504 | 80.80% | 19.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 66.40% | 32.80% | 0.00% | 0.83% | NA |
VI/Aromatic | 96 | 87.50% | 10.40% | 2.08% | 0.00% | NA |
Intermediate | 90 | 87.80% | 11.10% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0808162481 | G -> C | LOC_Os08g13710.2 | downstream_gene_variant ; 2829.0bp to feature; MODIFIER | silent_mutation | Average:48.89; most accessible tissue: Callus, score: 91.46 | N | N | N | N |
vg0808162481 | G -> C | LOC_Os08g13699.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.89; most accessible tissue: Callus, score: 91.46 | N | N | N | N |
vg0808162481 | G -> DEL | N | N | silent_mutation | Average:48.89; most accessible tissue: Callus, score: 91.46 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0808162481 | NA | 2.02E-07 | mr1345 | 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 |
vg0808162481 | NA | 2.19E-06 | mr1427 | 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 |
vg0808162481 | NA | 6.54E-06 | mr1759 | 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 |
vg0808162481 | 8.28E-06 | 7.15E-08 | mr1876 | 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 |