Variant ID: vg0426972613 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 26972613 |
Reference Allele: G | Alternative Allele: C,T |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 123. )
GCATTGGCAGGTGGAGTATATACCGTACCCTCCCCCCCTTTTTTTCCTTTCTTCTTCTTTTTTCCATTTATATATATAATGGATATATTTTTTAAATAAT[G/C,T]
ATAATTTTACAAACAAAGAATCTACCATCATATAACTTAAGCCGGTGTACTTTTTACTCTGTACTATTATTTTCAAATAATGCACTATTTTAAAATAAAT
ATTTATTTTAAAATAGTGCATTATTTGAAAATAATAGTACAGAGTAAAAAGTACACCGGCTTAAGTTATATGATGGTAGATTCTTTGTTTGTAAAATTAT[C/G,A]
ATTATTTAAAAAATATATCCATTATATATATAAATGGAAAAAAGAAGAAGAAAGGAAAAAAAGGGGGGGAGGGTACGGTATATACTCCACCTGCCAATGC
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 66.00% | 8.60% | 16.57% | 8.78% | T: 0.02% |
All Indica | 2759 | 42.70% | 14.40% | 28.05% | 14.79% | NA |
All Japonica | 1512 | 99.80% | 0.00% | 0.07% | 0.13% | NA |
Aus | 269 | 99.30% | 0.40% | 0.00% | 0.00% | T: 0.37% |
Indica I | 595 | 33.90% | 9.10% | 28.91% | 28.07% | NA |
Indica II | 465 | 25.40% | 18.50% | 35.05% | 21.08% | NA |
Indica III | 913 | 56.10% | 15.00% | 24.21% | 4.71% | NA |
Indica Intermediate | 786 | 44.10% | 15.40% | 27.74% | 12.72% | NA |
Temperate Japonica | 767 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
Tropical Japonica | 504 | 99.80% | 0.00% | 0.00% | 0.20% | NA |
Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 77.80% | 7.80% | 8.89% | 5.56% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0426972613 | G -> C | LOC_Os04g45580.1 | upstream_gene_variant ; 4531.0bp to feature; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> C | LOC_Os04g45590.1 | upstream_gene_variant ; 2986.0bp to feature; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> C | LOC_Os04g45600.1 | upstream_gene_variant ; 4792.0bp to feature; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> C | LOC_Os04g45580-LOC_Os04g45590 | intergenic_region ; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> DEL | N | N | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> T | LOC_Os04g45580.1 | upstream_gene_variant ; 4531.0bp to feature; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> T | LOC_Os04g45590.1 | upstream_gene_variant ; 2986.0bp to feature; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> T | LOC_Os04g45600.1 | upstream_gene_variant ; 4792.0bp to feature; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
vg0426972613 | G -> T | LOC_Os04g45580-LOC_Os04g45590 | intergenic_region ; MODIFIER | silent_mutation | Average:8.834; most accessible tissue: Minghui63 flower, score: 13.501 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0426972613 | NA | 3.07E-06 | Spikelet_length | Ind_All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0426972613 | NA | 9.65E-08 | mr1796 | 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 |