Variant ID: vg1002252247 (JBrowse) | Variation Type: SNP |
Chromosome: chr10 | Position: 2252247 |
Reference Allele: A | Alternative Allele: T |
Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.74, T: 0.26, others allele: 0.00, population size: 88. )
AGTTGCCGCCGTTGCCGCAGAGCTGCGCCAGTAGTTCGCCGGCGGCGAGCGGCATGATGCTAAGGAGGAGCAGGACGCCGACCATGGCGAACGACGGTTT[A/T]
CCTGTAGTTGCATGCTTGGTGTTTTATCCGGAATCAACCTGTAGAGATTTTTTTTTTCAAAAAAGAAATAAATAAAATGGTAATGAAACAATACTCCCAG
CTGGGAGTATTGTTTCATTACCATTTTATTTATTTCTTTTTTGAAAAAAAAAATCTCTACAGGTTGATTCCGGATAAAACACCAAGCATGCAACTACAGG[T/A]
AAACCGTCGTTCGCCATGGTCGGCGTCCTGCTCCTCCTTAGCATCATGCCGCTCGCCGCCGGCGAACTACTGGCGCAGCTCTGCGGCAACGGCGGCAACT
Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 61.60% | 38.40% | 0.00% | 0.00% | NA |
All Indica | 2759 | 83.50% | 16.50% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 15.90% | 84.10% | 0.00% | 0.00% | NA |
Aus | 269 | 86.20% | 13.80% | 0.00% | 0.00% | NA |
Indica I | 595 | 67.10% | 32.90% | 0.00% | 0.00% | NA |
Indica II | 465 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
Indica III | 913 | 82.80% | 17.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 89.20% | 10.80% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 8.90% | 91.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 22.20% | 77.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 25.30% | 74.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
Intermediate | 90 | 56.70% | 43.30% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1002252247 | A -> T | LOC_Os10g04720.1 | upstream_gene_variant ; 16.0bp to feature; MODIFIER | silent_mutation | Average:68.858; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
vg1002252247 | A -> T | LOC_Os10g04710.1 | downstream_gene_variant ; 3723.0bp to feature; MODIFIER | silent_mutation | Average:68.858; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
vg1002252247 | A -> T | LOC_Os10g04720-LOC_Os10g04730 | intergenic_region ; MODIFIER | silent_mutation | Average:68.858; most accessible tissue: Minghui63 flag leaf, score: 85.67 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1002252247 | 2.15E-08 | NA | mr1486 | 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 |
vg1002252247 | 1.90E-08 | 3.25E-24 | mr1548 | 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 |
vg1002252247 | NA | 1.32E-19 | mr1588 | 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 |
vg1002252247 | NA | 1.13E-06 | mr1709 | Ind_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 |
vg1002252247 | 3.06E-07 | NA | mr1486_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 |
vg1002252247 | NA | 1.94E-11 | mr1709_2 | Ind_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 |