Variant ID: vg0718640985 (JBrowse) | Variation Type: INDEL |
Chromosome: chr07 | Position: 18640985 |
Reference Allele: CGT | Alternative Allele: TGT,C |
Primary Allele: TGT | Secondary Allele: CGT |
Inferred Ancestral Allele: Not determined.
TATCAACAAGTCTTATTATTGTAATATTTCTAAATGTTTTACAATATAGTCATAAACATATCTGATAATTAGTTATCCAGGGTTTGCCTCTTTAAACCTG[CGT/TGT,C]
ACAGATACATATGGCTCCTTACGATTTTCCTCACCGTGGCAACTTTATGACTTAAGCATGACTATAATCATGCTATCGGTGATAACGTCTAACTATTCCT
AGGAATAGTTAGACGTTATCACCGATAGCATGATTATAGTCATGCTTAAGTCATAAAGTTGCCACGGTGAGGAAAATCGTAAGGAGCCATATGTATCTGT[ACG/ACA,G]
CAGGTTTAAAGAGGCAAACCCTGGATAACTAATTATCAGATATGTTTATGACTATATTGTAAAACATTTAGAAATATTACAATAATAAGACTTGTTGATA
Populations | Population Size | Frequency of TGT(primary allele) | Frequency of CGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 85.80% | 12.60% | 1.52% | 0.00% | C: 0.04% |
All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 57.30% | 38.20% | 4.56% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 24.10% | 68.60% | 7.30% | 0.00% | NA |
Tropical Japonica | 504 | 97.60% | 0.80% | 1.59% | 0.00% | NA |
Japonica Intermediate | 241 | 78.40% | 19.50% | 2.07% | 0.00% | NA |
VI/Aromatic | 96 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
Intermediate | 90 | 85.60% | 8.90% | 3.33% | 0.00% | C: 2.22% |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0718640985 | CGT -> TGT | LOC_Os07g31450.1 | upstream_gene_variant ; 2306.0bp to feature; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
vg0718640985 | CGT -> TGT | LOC_Os07g31460.1 | upstream_gene_variant ; 2035.0bp to feature; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
vg0718640985 | CGT -> TGT | LOC_Os07g31460.2 | upstream_gene_variant ; 2035.0bp to feature; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
vg0718640985 | CGT -> TGT | LOC_Os07g31450-LOC_Os07g31460 | intergenic_region ; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
vg0718640985 | CGT -> C | LOC_Os07g31450.1 | upstream_gene_variant ; 2307.0bp to feature; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
vg0718640985 | CGT -> C | LOC_Os07g31460.1 | upstream_gene_variant ; 2034.0bp to feature; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
vg0718640985 | CGT -> C | LOC_Os07g31460.2 | upstream_gene_variant ; 2034.0bp to feature; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
vg0718640985 | CGT -> C | LOC_Os07g31450-LOC_Os07g31460 | intergenic_region ; MODIFIER | silent_mutation | Average:62.751; most accessible tissue: Callus, score: 81.649 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0718640985 | 1.19E-08 | NA | Grain_weight | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0718640985 | NA | 2.17E-12 | mr1741 | 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 |
vg0718640985 | NA | 1.00E-09 | mr1011_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 |