Variant ID: vg0209726556 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 9726556 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AGATTGCTCATACTGATTCCGTAATTGAATACGTGTTTTAGTGATCCTCCATTTCCTTTTGGAGAAAATCCCTTGTATACGGTATACCTCTGAAATTTTA[C/A]
CTAATCCCTTCTATGCCCCTAAATTTTGCTTACTTCCTTATATACCCCTAAAATTTGATTTTGATCCCTTGCATACCCCTCCCGTCAGTTGACCGTTTAT
ATAAACGGTCAACTGACGGGAGGGGTATGCAAGGGATCAAAATCAAATTTTAGGGGTATATAAGGAAGTAAGCAAAATTTAGGGGCATAGAAGGGATTAG[G/T]
TAAAATTTCAGAGGTATACCGTATACAAGGGATTTTCTCCAAAAGGAAATGGAGGATCACTAAAACACGTATTCAATTACGGAATCAGTATGAGCAATCT
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 | 57.40% | 8.70% | 3.11% | 30.83% | NA |
All Indica | 2759 | 58.60% | 0.30% | 2.10% | 39.04% | NA |
All Japonica | 1512 | 62.50% | 20.40% | 4.76% | 12.30% | NA |
Aus | 269 | 21.90% | 13.80% | 4.83% | 59.48% | NA |
Indica I | 595 | 63.20% | 0.20% | 3.36% | 33.28% | NA |
Indica II | 465 | 52.00% | 0.20% | 1.94% | 45.81% | NA |
Indica III | 913 | 57.80% | 0.00% | 1.31% | 40.85% | NA |
Indica Intermediate | 786 | 59.80% | 0.80% | 2.16% | 37.28% | NA |
Temperate Japonica | 767 | 84.50% | 1.80% | 3.78% | 9.91% | NA |
Tropical Japonica | 504 | 32.70% | 48.20% | 3.17% | 15.87% | NA |
Japonica Intermediate | 241 | 54.80% | 21.60% | 11.20% | 12.45% | NA |
VI/Aromatic | 96 | 37.50% | 46.90% | 4.17% | 11.46% | NA |
Intermediate | 90 | 63.30% | 11.10% | 0.00% | 25.56% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0209726556 | C -> A | LOC_Os02g17020.1 | upstream_gene_variant ; 3636.0bp to feature; MODIFIER | silent_mutation | Average:27.883; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |
vg0209726556 | C -> A | LOC_Os02g17010-LOC_Os02g17020 | intergenic_region ; MODIFIER | silent_mutation | Average:27.883; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |
vg0209726556 | C -> DEL | N | N | silent_mutation | Average:27.883; most accessible tissue: Zhenshan97 flag leaf, score: 63.101 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0209726556 | 1.01E-06 | NA | mr1113 | 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 |