Variant ID: vg0112438971 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 12438971 |
Reference Allele: T | Alternative Allele: G |
Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 105. )
CCGTTTATTTTATTTTGCGCTGCTTAGATCTTTATTGTTTGAGAGGAACTATCTACCTCTGTAATGACTTTATATTCGCTTATTAATTAGAGTAACAATT[T/G]
TACTCTATTATCAATTTGTTATTGTGTGCCTCGGCTGATTCCTGGATGAGGGTTTACATACATGTAAGCGTTTGGAATTTTGGATAGAAATTCCGGGCGT
ACGCCCGGAATTTCTATCCAAAATTCCAAACGCTTACATGTATGTAAACCCTCATCCAGGAATCAGCCGAGGCACACAATAACAAATTGATAATAGAGTA[A/C]
AATTGTTACTCTAATTAATAAGCGAATATAAAGTCATTACAGAGGTAGATAGTTCCTCTCAAACAATAAAGATCTAAGCAGCGCAAAATAAAATAAACGG
Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 68.20% | 31.00% | 0.04% | 0.72% | NA |
All Indica | 2759 | 96.70% | 3.30% | 0.04% | 0.00% | NA |
All Japonica | 1512 | 13.60% | 84.10% | 0.00% | 2.25% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 95.30% | 4.70% | 0.00% | 0.00% | NA |
Indica III | 913 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.10% | 2.80% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 6.10% | 93.90% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 12.70% | 80.60% | 0.00% | 6.75% | NA |
Japonica Intermediate | 241 | 39.40% | 60.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 31.20% | 68.80% | 0.00% | 0.00% | NA |
Intermediate | 90 | 57.80% | 41.10% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0112438971 | T -> G | LOC_Os01g22140.1 | downstream_gene_variant ; 54.0bp to feature; MODIFIER | silent_mutation | Average:25.861; most accessible tissue: Minghui63 root, score: 33.152 | N | N | N | N |
vg0112438971 | T -> G | LOC_Os01g22120-LOC_Os01g22140 | intergenic_region ; MODIFIER | silent_mutation | Average:25.861; most accessible tissue: Minghui63 root, score: 33.152 | N | N | N | N |
vg0112438971 | T -> DEL | N | N | silent_mutation | Average:25.861; most accessible tissue: Minghui63 root, score: 33.152 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0112438971 | NA | 2.61E-06 | mr1066 | 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 |
vg0112438971 | NA | 9.04E-19 | mr1242 | 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 |
vg0112438971 | NA | 2.57E-14 | mr1361 | 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 |
vg0112438971 | NA | 1.10E-18 | mr1168_2 | 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 |
vg0112438971 | NA | 5.67E-19 | mr1657_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 |