Variant ID: vg1227357645 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 27357645 |
Reference Allele: T | Alternative Allele: A |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, A: 0.06, others allele: 0.00, population size: 218. )
CTCCTTTTTCTGCTGTTAGGTTATTTCAGGAAGATTGCTTCTGTAGTTCAGTTAACCCTCCCTTCTCAGGGGTGGCTCTTTTGCTTTCAATTTTTATCCT[T/A]
GGTTATGTAACAGGGTTTATCCCCTAATTCTATTCTTGCTTAATAAAGTTGATGTGTTTTTTTTTAAAAAAAGCAAATCCACCTGCAAAAATACATAGGG
CCCTATGTATTTTTGCAGGTGGATTTGCTTTTTTTAAAAAAAAACACATCAACTTTATTAAGCAAGAATAGAATTAGGGGATAAACCCTGTTACATAACC[A/T]
AGGATAAAAATTGAAAGCAAAAGAGCCACCCCTGAGAAGGGAGGGTTAACTGAACTACAGAAGCAATCTTCCTGAAATAACCTAACAGCAGAAAAAGGAG
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 74.00% | 25.90% | 0.11% | 0.00% | NA |
All Indica | 2759 | 59.30% | 40.60% | 0.14% | 0.00% | NA |
All Japonica | 1512 | 94.90% | 5.00% | 0.07% | 0.00% | NA |
Aus | 269 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 79.00% | 20.80% | 0.17% | 0.00% | NA |
Indica II | 465 | 79.10% | 20.90% | 0.00% | 0.00% | NA |
Indica III | 913 | 38.90% | 61.00% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 56.40% | 43.40% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 91.40% | 8.50% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 95.90% | 4.10% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 86.70% | 13.30% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1227357645 | T -> A | LOC_Os12g44110.2 | downstream_gene_variant ; 1779.0bp to feature; MODIFIER | silent_mutation | Average:60.699; most accessible tissue: Zhenshan97 flower, score: 83.915 | N | N | N | N |
vg1227357645 | T -> A | LOC_Os12g44100-LOC_Os12g44110 | intergenic_region ; MODIFIER | silent_mutation | Average:60.699; most accessible tissue: Zhenshan97 flower, score: 83.915 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1227357645 | 2.86E-06 | 2.86E-06 | mr1024 | Jap_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 |
vg1227357645 | NA | 2.14E-06 | mr1565 | Jap_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 |
vg1227357645 | NA | 4.65E-06 | mr1922 | Jap_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 |
vg1227357645 | NA | 1.77E-06 | mr1940 | Jap_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 |
vg1227357645 | 2.13E-07 | 2.13E-07 | mr1024_2 | Jap_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 |
vg1227357645 | NA | 2.83E-07 | mr1565_2 | Jap_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 |
vg1227357645 | 1.66E-06 | 1.66E-06 | mr1915_2 | Jap_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 |