Variant ID: vg0114208243 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 14208243 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AAATGCAACAAGATCTTAGTATAAAGGCAGATTTAACATGTCAATCAAGCATATAAGATAGAAGTAGTTAAATCAGGTAAGGTCGGCTGAAACCCCGATG[G/C]
TACCCTAATCGGCAACCAAAAGCAGGCTAGAGATTGAGATTCTAATCACGACTTATAAGGTCAAACTCAACTGATGCATCTATAAGTATGAAAATAAAGA
TCTTTATTTTCATACTTATAGATGCATCAGTTGAGTTTGACCTTATAAGTCGTGATTAGAATCTCAATCTCTAGCCTGCTTTTGGTTGCCGATTAGGGTA[C/G]
CATCGGGGTTTCAGCCGACCTTACCTGATTTAACTACTTCTATCTTATATGCTTGATTGACATGTTAAATCTGCCTTTATACTAAGATCTTGTTGCATTT
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 54.70% | 3.00% | 7.53% | 34.70% | NA |
All Indica | 2759 | 31.20% | 4.90% | 10.66% | 53.17% | NA |
All Japonica | 1512 | 95.50% | 0.00% | 0.66% | 3.84% | NA |
Aus | 269 | 61.70% | 1.90% | 14.50% | 21.93% | NA |
Indica I | 595 | 32.40% | 0.00% | 10.59% | 56.97% | NA |
Indica II | 465 | 23.00% | 11.80% | 10.97% | 54.19% | NA |
Indica III | 913 | 35.00% | 5.50% | 9.97% | 49.51% | NA |
Indica Intermediate | 786 | 30.80% | 3.90% | 11.32% | 53.94% | NA |
Temperate Japonica | 767 | 98.40% | 0.00% | 0.13% | 1.43% | NA |
Tropical Japonica | 504 | 89.50% | 0.00% | 1.59% | 8.93% | NA |
Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
VI/Aromatic | 96 | 60.40% | 0.00% | 3.12% | 36.46% | NA |
Intermediate | 90 | 63.30% | 2.20% | 11.11% | 23.33% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0114208243 | G -> DEL | N | N | silent_mutation | Average:8.287; most accessible tissue: Callus, score: 31.438 | N | N | N | N |
vg0114208243 | G -> C | LOC_Os01g25160.1 | downstream_gene_variant ; 2236.0bp to feature; MODIFIER | silent_mutation | Average:8.287; most accessible tissue: Callus, score: 31.438 | N | N | N | N |
vg0114208243 | G -> C | LOC_Os01g25150-LOC_Os01g25160 | intergenic_region ; MODIFIER | silent_mutation | Average:8.287; most accessible tissue: Callus, score: 31.438 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0114208243 | NA | 5.14E-06 | mr1448 | 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 |
vg0114208243 | 6.55E-06 | 2.60E-06 | mr1677 | 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 |