Variant ID: vg0114147236 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 14147236 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.09, others allele: 0.00, population size: 86. )
CTATTTTTCAGAGTTTACTTAGGGCTTCAACTCCAAAATTTAGCTACAGGAGTTGGTTCTGGAGTAGAGTTATGGAGCTTCCTAAACTCAGCTCTACCTC[T/C]
CTAGTTTATTTTGTGAGAGAGCTCTACCCAGCTCCGCTCCCCTTTTAGGTAAAGCTGAAACTGTTTGGCTGAGCTCCAGCTCCAGGAGGAGAGATAGGGT
ACCCTATCTCTCCTCCTGGAGCTGGAGCTCAGCCAAACAGTTTCAGCTTTACCTAAAAGGGGAGCGGAGCTGGGTAGAGCTCTCTCACAAAATAAACTAG[A/G]
GAGGTAGAGCTGAGTTTAGGAAGCTCCATAACTCTACTCCAGAACCAACTCCTGTAGCTAAATTTTGGAGTTGAAGCCCTAAGTAAACTCTGAAAAATAG
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 58.80% | 29.40% | 0.21% | 11.60% | NA |
All Indica | 2759 | 37.60% | 42.70% | 0.33% | 19.43% | NA |
All Japonica | 1512 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
Aus | 269 | 68.80% | 31.20% | 0.00% | 0.00% | NA |
Indica I | 595 | 59.50% | 39.80% | 0.17% | 0.50% | NA |
Indica II | 465 | 45.60% | 12.70% | 0.00% | 41.72% | NA |
Indica III | 913 | 16.00% | 61.20% | 0.22% | 22.56% | NA |
Indica Intermediate | 786 | 41.30% | 41.00% | 0.76% | 16.92% | NA |
Temperate Japonica | 767 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 89.70% | 10.30% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 52.10% | 46.90% | 0.00% | 1.04% | NA |
Intermediate | 90 | 73.30% | 13.30% | 1.11% | 12.22% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0114147236 | T -> DEL | N | N | silent_mutation | Average:26.709; most accessible tissue: Callus, score: 72.702 | N | N | N | N |
vg0114147236 | T -> C | LOC_Os01g25070.1 | upstream_gene_variant ; 2753.0bp to feature; MODIFIER | silent_mutation | Average:26.709; most accessible tissue: Callus, score: 72.702 | N | N | N | N |
vg0114147236 | T -> C | LOC_Os01g25065-LOC_Os01g25070 | intergenic_region ; MODIFIER | silent_mutation | Average:26.709; most accessible tissue: Callus, score: 72.702 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0114147236 | NA | 7.82E-06 | mr1064 | 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 |
vg0114147236 | NA | 1.21E-07 | mr1193 | 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 |
vg0114147236 | 1.23E-06 | 4.27E-08 | mr1637 | 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 |
vg0114147236 | NA | 1.34E-10 | mr1519_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 |