Variant ID: vg0310499546 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 10499546 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 277. )
AAGATCAAACTAAAATAAGAAGAGCACATTTATTCAAGTCTATTTGTGAATCTCCATCCATAGTTTGCAAAGAGTTGTATGACCGTTGTCTTAAGCCTAC[C/A]
ACATGCAACCTTCATAAGCACTCTATCATCTTCACACATTTGCAGCTGAATCGCCTCCGTGTCTAATCCCACGGTCTGACGGTCATATGCTTATGCCCGA
TCGGGCATAAGCATATGACCGTCAGACCGTGGGATTAGACACGGAGGCGATTCAGCTGCAAATGTGTGAAGATGATAGAGTGCTTATGAAGGTTGCATGT[G/T]
GTAGGCTTAAGACAACGGTCATACAACTCTTTGCAAACTATGGATGGAGATTCACAAATAGACTTGAATAAATGTGCTCTTCTTATTTTAGTTTGATCTT
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 91.80% | 8.20% | 0.02% | 0.00% | NA |
All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 76.30% | 23.70% | 0.07% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 39.50% | 60.50% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 79.70% | 19.90% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 83.30% | 16.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0310499546 | C -> A | LOC_Os03g18740.1 | upstream_gene_variant ; 2469.0bp to feature; MODIFIER | silent_mutation | Average:55.752; most accessible tissue: Callus, score: 76.776 | N | N | N | N |
vg0310499546 | C -> A | LOC_Os03g18729-LOC_Os03g18740 | intergenic_region ; MODIFIER | silent_mutation | Average:55.752; most accessible tissue: Callus, score: 76.776 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0310499546 | NA | 6.84E-06 | mr1083 | 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 |
vg0310499546 | NA | 3.58E-06 | mr1852 | 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 |
vg0310499546 | 2.43E-07 | NA | mr1925 | 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 |
vg0310499546 | 1.09E-06 | 2.52E-08 | mr1925 | 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 |
vg0310499546 | NA | 4.19E-09 | mr1454_2 | 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 |
vg0310499546 | NA | 7.13E-09 | mr1696_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 |
vg0310499546 | NA | 7.04E-09 | mr1905_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 |