Variant ID: vg0507079626 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 7079626 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.00, others allele: 0.00, population size: 295. )
TCTGGTGGTCCGCTCCGGGTGGAGGCTCCAAATATCTCATTTTTGGTTTCTCTGCTGCTTCATTCTGTGCTAGATCAGTTTGTCCTGGAAATTTATAGAT[C/A]
ACTGATGCTCTGTAAGATAATGTCATATTCCTCTTGATCACGGCTACCGTACAGAAGCAACAATTTCGATCACGGACAAAGCTTCCACGAACTGCAATGT
ACATTGCAGTTCGTGGAAGCTTTGTCCGTGATCGAAATTGTTGCTTCTGTACGGTAGCCGTGATCAAGAGGAATATGACATTATCTTACAGAGCATCAGT[G/T]
ATCTATAAATTTCCAGGACAAACTGATCTAGCACAGAATGAAGCAGCAGAGAAACCAAAAATGAGATATTTGGAGCCTCCACCCGGAGCGGACCACCAGA
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Aus | 269 | 48.30% | 51.70% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 89.60% | 10.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 94.40% | 5.60% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0507079626 | C -> A | LOC_Os05g12310.1 | upstream_gene_variant ; 1268.0bp to feature; MODIFIER | silent_mutation | Average:57.444; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
vg0507079626 | C -> A | LOC_Os05g12320.1 | upstream_gene_variant ; 3257.0bp to feature; MODIFIER | silent_mutation | Average:57.444; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
vg0507079626 | C -> A | LOC_Os05g12310-LOC_Os05g12320 | intergenic_region ; MODIFIER | silent_mutation | Average:57.444; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0507079626 | NA | 1.72E-07 | mr1157 | 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 |
vg0507079626 | NA | 9.94E-06 | mr1373 | 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 |
vg0507079626 | NA | 1.26E-08 | mr1446 | 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 |
vg0507079626 | NA | 4.39E-07 | mr1652 | 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 |
vg0507079626 | NA | 4.86E-06 | mr1608_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 |
vg0507079626 | 2.07E-06 | NA | mr1613_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 |
vg0507079626 | 1.93E-07 | NA | mr1962_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 |