Variant ID: vg0820586619 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 20586619 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 254. )
GACTAAGTGCCTCTTCTGTAAGTATTTTACGCTTTATTTATGTTTGAAACTGTATATTACTTGTCGCTTTATTTACGTTTGGAACTGTATATTACTTGTC[G/A]
TTTTGTGTACCCTGGCTGGTACTGGACAGGGATTTAATACACAAAATAGTCTGGAAATTTGGGTTAAATTTCTGGGCGTGACACTGGTGTTGGCCCATGT
ACATGGGCCAACACCAGTGTCACGCCCAGAAATTTAACCCAAATTTCCAGACTATTTTGTGTATTAAATCCCTGTCCAGTACCAGCCAGGGTACACAAAA[C/T]
GACAAGTAATATACAGTTCCAAACGTAAATAAAGCGACAAGTAATATACAGTTTCAAACATAAATAAAGCGTAAAATACTTACAGAAGAGGCACTTAGTC
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
All Indica | 2759 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 85.00% | 15.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0820586619 | G -> A | LOC_Os08g33120.1 | upstream_gene_variant ; 3123.0bp to feature; MODIFIER | silent_mutation | Average:67.066; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0820586619 | G -> A | LOC_Os08g33130.1 | upstream_gene_variant ; 1047.0bp to feature; MODIFIER | silent_mutation | Average:67.066; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0820586619 | G -> A | LOC_Os08g33140.1 | upstream_gene_variant ; 4840.0bp to feature; MODIFIER | silent_mutation | Average:67.066; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0820586619 | G -> A | LOC_Os08g33120.2 | upstream_gene_variant ; 4393.0bp to feature; MODIFIER | silent_mutation | Average:67.066; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0820586619 | G -> A | LOC_Os08g33120.3 | upstream_gene_variant ; 4393.0bp to feature; MODIFIER | silent_mutation | Average:67.066; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0820586619 | G -> A | LOC_Os08g33120.5 | upstream_gene_variant ; 4393.0bp to feature; MODIFIER | silent_mutation | Average:67.066; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
vg0820586619 | G -> A | LOC_Os08g33120-LOC_Os08g33130 | intergenic_region ; MODIFIER | silent_mutation | Average:67.066; most accessible tissue: Minghui63 flag leaf, score: 83.826 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0820586619 | 1.26E-06 | 1.48E-06 | mr1034 | Ind_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 |