Variant ID: vg0827076816 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 27076816 |
Reference Allele: A | Alternative Allele: G,T |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCATCGGCTCCTAGCCGATCGGCTATCATTTATGGATTTAATCTCGTTTTTCTTGTCTTTTATTCTTGTTGGTTGCAGGATCAAATCAACTGGCACGCTC[A/G,T]
CGAACCTAAAAGCAAGATTTTAGACCTGCACAGGAGTTAAGCAGATCTTCCAGGCCAGTGTGTGTTTTTCGCATCAACACCCTCCTTGCTGCTCTGGCCT
AGGCCAGAGCAGCAAGGAGGGTGTTGATGCGAAAAACACACACTGGCCTGGAAGATCTGCTTAACTCCTGTGCAGGTCTAAAATCTTGCTTTTAGGTTCG[T/C,A]
GAGCGTGCCAGTTGATTTGATCCTGCAACCAACAAGAATAAAAGACAAGAAAAACGAGATTAAATCCATAAATGATAGCCGATCGGCTAGGAGCCGATGA
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 67.80% | 11.80% | 1.69% | 18.73% | T: 0.02% |
All Indica | 2759 | 54.50% | 12.90% | 2.75% | 29.79% | T: 0.04% |
All Japonica | 1512 | 97.40% | 2.10% | 0.07% | 0.46% | NA |
Aus | 269 | 23.80% | 61.00% | 0.00% | 15.24% | NA |
Indica I | 595 | 59.70% | 13.80% | 1.68% | 24.71% | T: 0.17% |
Indica II | 465 | 54.00% | 13.30% | 3.23% | 29.46% | NA |
Indica III | 913 | 50.90% | 14.10% | 2.30% | 32.64% | NA |
Indica Intermediate | 786 | 55.10% | 10.60% | 3.82% | 30.53% | NA |
Temperate Japonica | 767 | 99.00% | 0.40% | 0.13% | 0.52% | NA |
Tropical Japonica | 504 | 94.00% | 5.80% | 0.00% | 0.20% | NA |
Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
VI/Aromatic | 96 | 92.70% | 2.10% | 0.00% | 5.21% | NA |
Intermediate | 90 | 81.10% | 4.40% | 3.33% | 11.11% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0827076816 | A -> G | LOC_Os08g42800.1 | upstream_gene_variant ; 4241.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> G | LOC_Os08g42810.1 | upstream_gene_variant ; 1488.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> G | LOC_Os08g42820.1 | downstream_gene_variant ; 74.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> G | LOC_Os08g42830.1 | downstream_gene_variant ; 3869.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> G | LOC_Os08g42810-LOC_Os08g42820 | intergenic_region ; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> T | LOC_Os08g42800.1 | upstream_gene_variant ; 4241.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> T | LOC_Os08g42810.1 | upstream_gene_variant ; 1488.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> T | LOC_Os08g42820.1 | downstream_gene_variant ; 74.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> T | LOC_Os08g42830.1 | downstream_gene_variant ; 3869.0bp to feature; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> T | LOC_Os08g42810-LOC_Os08g42820 | intergenic_region ; MODIFIER | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
vg0827076816 | A -> DEL | N | N | silent_mutation | Average:59.752; most accessible tissue: Minghui63 panicle, score: 71.773 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0827076816 | NA | 4.61E-06 | mr1734 | 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 |