Variant ID: vg0726684254 (JBrowse) | Variation Type: SNP |
Chromosome: chr07 | Position: 26684254 |
Reference Allele: T | Alternative Allele: C |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 309. )
CAGTTGATTTGCCGTCAATGTCTTAGCTAGGGCCTGCAAAATGTATGGACATTGCTTAAAATGGCTAGTTGGTGATGTCATCAGAGTCAAGACATATCGG[T/C]
ATAAGCCTACTTAAACTGCACAACCAAAAGCAATATATTGCTCGTACATGGATAACTTGACACATGTAAAAAATGAAAAAAAATATAAGCAGCAAGAATA
TATTCTTGCTGCTTATATTTTTTTTCATTTTTTACATGTGTCAAGTTATCCATGTACGAGCAATATATTGCTTTTGGTTGTGCAGTTTAAGTAGGCTTAT[A/G]
CCGATATGTCTTGACTCTGATGACATCACCAACTAGCCATTTTAAGCAATGTCCATACATTTTGCAGGCCCTAGCTAAGACATTGACGGCAAATCAACTG
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 89.00% | 11.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.10% | 3.90% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 80.10% | 19.90% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 95.60% | 4.40% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0726684254 | T -> C | LOC_Os07g44700.1 | upstream_gene_variant ; 4118.0bp to feature; MODIFIER | silent_mutation | Average:59.094; most accessible tissue: Callus, score: 86.969 | N | N | N | N |
vg0726684254 | T -> C | LOC_Os07g44710.1 | intron_variant ; MODIFIER | silent_mutation | Average:59.094; most accessible tissue: Callus, score: 86.969 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0726684254 | NA | 1.52E-07 | 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 |
vg0726684254 | NA | 7.36E-06 | mr1153_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 |
vg0726684254 | 1.41E-06 | NA | mr1252_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 |
vg0726684254 | NA | 2.73E-06 | mr1383_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 |