Variant ID: vg0801293540 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 1293540 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.00, others allele: 0.00, population size: 263. )
ACGTGACAAAATATCATCAAATAGAACCAATCAACGAAACTTTCCAGATCTGATCTTTGAAGTATTAGAAAAGTTTTGGATGAATTAACTTGAACAAAAT[C/T]
GCAGCAAAATGAACAATCACAAGTTAATACCAAAACCAAATATAAACGTAAAACTTACGAAACCGGAATAGATCGTTAATGCCTTGATGATTGAATATGA
TCATATTCAATCATCAAGGCATTAACGATCTATTCCGGTTTCGTAAGTTTTACGTTTATATTTGGTTTTGGTATTAACTTGTGATTGTTCATTTTGCTGC[G/A]
ATTTTGTTCAAGTTAATTCATCCAAAACTTTTCTAATACTTCAAAGATCAGATCTGGAAAGTTTCGTTGATTGGTTCTATTTGATGATATTTTGTCACGT
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 89.30% | 10.70% | 0.00% | 0.00% | NA |
All Indica | 2759 | 91.20% | 8.80% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Aus | 269 | 16.70% | 83.30% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 84.80% | 15.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 88.00% | 12.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 76.00% | 24.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 90.00% | 10.00% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0801293540 | C -> T | LOC_Os08g02970.1 | upstream_gene_variant ; 554.0bp to feature; MODIFIER | silent_mutation | Average:58.837; most accessible tissue: Callus, score: 75.885 | N | N | N | N |
vg0801293540 | C -> T | LOC_Os08g02980.1 | upstream_gene_variant ; 3459.0bp to feature; MODIFIER | silent_mutation | Average:58.837; most accessible tissue: Callus, score: 75.885 | N | N | N | N |
vg0801293540 | C -> T | LOC_Os08g02970-LOC_Os08g02980 | intergenic_region ; MODIFIER | silent_mutation | Average:58.837; most accessible tissue: Callus, score: 75.885 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0801293540 | NA | 2.89E-10 | mr1587 | 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 |
vg0801293540 | NA | 4.88E-08 | mr1803 | 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 |
vg0801293540 | NA | 9.79E-09 | mr1166_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 |
vg0801293540 | NA | 2.09E-16 | mr1587_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 |
vg0801293540 | NA | 7.41E-12 | mr1803_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 |