Variant ID: vg0127893586 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 27893586 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.67, G: 0.31, others allele: 0.00, population size: 45. )
GGTCGCACGCTTAATGGGTCGGAATAAGGGGATTGGATGGAGATCCAATATGAGCTTACTTCGGATAGGGATCCGAATAGGAGTCCTACGGGCTTTGAAG[G/A]
CCCGAGTGATGGATCCTATATATTCGTGAGAGGTGTGACCGGCGGAGGCATTGCATCACGTGAGAAACCCTAGCCGTCACTTCCCTCCCCGAGCAAAACC
GGTTTTGCTCGGGGAGGGAAGTGACGGCTAGGGTTTCTCACGTGATGCAATGCCTCCGCCGGTCACACCTCTCACGAATATATAGGATCCATCACTCGGG[C/T]
CTTCAAAGCCCGTAGGACTCCTATTCGGATCCCTATCCGAAGTAAGCTCATATTGGATCTCCATCCAATCCCCTTATTCCGACCCATTAAGCGTGCGACC
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 | 70.60% | 29.30% | 0.04% | 0.00% | NA |
All Indica | 2759 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 13.80% | 86.20% | 0.00% | 0.00% | NA |
Aus | 269 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 98.20% | 1.80% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 0.30% | 99.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 37.90% | 62.10% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 6.60% | 93.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 55.60% | 42.20% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0127893586 | G -> A | LOC_Os01g48660.1 | upstream_gene_variant ; 2768.0bp to feature; MODIFIER | silent_mutation | Average:56.015; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
vg0127893586 | G -> A | LOC_Os01g48650.1 | intron_variant ; MODIFIER | silent_mutation | Average:56.015; most accessible tissue: Minghui63 panicle, score: 77.956 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0127893586 | NA | 9.90E-15 | 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 |
vg0127893586 | 9.09E-07 | NA | mr1103_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 |
vg0127893586 | 8.09E-06 | NA | mr1104_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 |
vg0127893586 | NA | 7.69E-24 | mr1308_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 |
vg0127893586 | NA | 7.97E-23 | mr1361_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 |
vg0127893586 | NA | 6.27E-28 | mr1584_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 |
vg0127893586 | NA | 2.09E-07 | mr1607_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 |
vg0127893586 | NA | 9.43E-17 | mr1730_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 |