Variant ID: vg0624711737 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 24711737 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATTTCACTAAGTTACTTCTTAGACATATAAAAGTAAATTTAGTAAAGGTTAAAAGTAATTTACATATATATTACAGAAGTAACTTATAATAAAAAGGAAA[G/A]
TAACTTTAATTTAGAACTATATCTAGATTCATTAACATCTATATAAATATGGGCAATGCTAAAATAACTTATATTATGAAACGGGGGAGTAACTCTCTTT
AAAGAGAGTTACTCCCCCGTTTCATAATATAAGTTATTTTAGCATTGCCCATATTTATATAGATGTTAATGAATCTAGATATAGTTCTAAATTAAAGTTA[C/T]
TTTCCTTTTTATTATAAGTTACTTCTGTAATATATATGTAAATTACTTTTAACCTTTACTAAATTTACTTTTATATGTCTAAGAAGTAACTTAGTGAAAT
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 49.60% | 0.10% | 7.17% | 43.08% | NA |
All Indica | 2759 | 23.30% | 0.10% | 10.22% | 66.36% | NA |
All Japonica | 1512 | 99.30% | 0.00% | 0.07% | 0.60% | NA |
Aus | 269 | 23.80% | 0.40% | 17.10% | 58.74% | NA |
Indica I | 595 | 14.60% | 0.00% | 10.76% | 74.62% | NA |
Indica II | 465 | 18.10% | 0.00% | 8.17% | 73.76% | NA |
Indica III | 913 | 31.10% | 0.40% | 10.73% | 57.72% | NA |
Indica Intermediate | 786 | 23.80% | 0.00% | 10.43% | 65.78% | NA |
Temperate Japonica | 767 | 98.80% | 0.00% | 0.13% | 1.04% | NA |
Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 85.40% | 0.00% | 3.12% | 11.46% | NA |
Intermediate | 90 | 62.20% | 0.00% | 7.78% | 30.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0624711737 | G -> A | LOC_Os06g41300.1 | upstream_gene_variant ; 772.0bp to feature; MODIFIER | silent_mutation | Average:10.228; most accessible tissue: Callus, score: 30.323 | N | N | N | N |
vg0624711737 | G -> A | LOC_Os06g41310.1 | upstream_gene_variant ; 4121.0bp to feature; MODIFIER | silent_mutation | Average:10.228; most accessible tissue: Callus, score: 30.323 | N | N | N | N |
vg0624711737 | G -> A | LOC_Os06g41290.1 | downstream_gene_variant ; 4196.0bp to feature; MODIFIER | silent_mutation | Average:10.228; most accessible tissue: Callus, score: 30.323 | N | N | N | N |
vg0624711737 | G -> A | LOC_Os06g41290-LOC_Os06g41300 | intergenic_region ; MODIFIER | silent_mutation | Average:10.228; most accessible tissue: Callus, score: 30.323 | N | N | N | N |
vg0624711737 | G -> DEL | N | N | silent_mutation | Average:10.228; most accessible tissue: Callus, score: 30.323 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0624711737 | 6.17E-07 | 4.63E-06 | mr1645_2 | 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 |