Variant ID: vg0224219685 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 24219685 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.85, C: 0.16, others allele: 0.00, population size: 94. )
TTGAAATCTAGGGTATTTTCAGGTGACCAAAATTTACAAGTCCTATATCTCAAATGCTTGTTTTGAAGTTATACGGTACTCGGTGCTTATGATACTACTT[C/T]
CATTTCAAGTTATAAGACGTTTTGACTTTGGTCAAAGTCAAGCTGCTTCAAGTTTGTAGAAAAAATAACAATATTTTCAGCCCAAGATAAATTTATTATG
CATAATAAATTTATCTTGGGCTGAAAATATTGTTATTTTTTCTACAAACTTGAAGCAGCTTGACTTTGACCAAAGTCAAAACGTCTTATAACTTGAAATG[G/A]
AAGTAGTATCATAAGCACCGAGTACCGTATAACTTCAAAACAAGCATTTGAGATATAGGACTTGTAAATTTTGGTCACCTGAAAATACCCTAGATTTCAA
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 59.90% | 39.60% | 0.47% | 0.02% | NA |
All Indica | 2759 | 43.70% | 55.80% | 0.51% | 0.04% | NA |
All Japonica | 1512 | 90.60% | 8.90% | 0.46% | 0.00% | NA |
Aus | 269 | 48.00% | 52.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 39.80% | 59.30% | 0.84% | 0.00% | NA |
Indica II | 465 | 58.70% | 40.90% | 0.22% | 0.22% | NA |
Indica III | 913 | 30.10% | 69.70% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 53.40% | 45.80% | 0.76% | 0.00% | NA |
Temperate Japonica | 767 | 89.40% | 9.80% | 0.78% | 0.00% | NA |
Tropical Japonica | 504 | 92.10% | 7.70% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 91.30% | 8.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 58.30% | 41.70% | 0.00% | 0.00% | NA |
Intermediate | 90 | 78.90% | 20.00% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0224219685 | C -> T | LOC_Os02g40010.1 | upstream_gene_variant ; 3620.0bp to feature; MODIFIER | silent_mutation | Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
vg0224219685 | C -> T | LOC_Os02g40010.2 | upstream_gene_variant ; 3620.0bp to feature; MODIFIER | silent_mutation | Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
vg0224219685 | C -> T | LOC_Os02g40010.3 | upstream_gene_variant ; 3620.0bp to feature; MODIFIER | silent_mutation | Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
vg0224219685 | C -> T | LOC_Os02g40010.4 | upstream_gene_variant ; 3620.0bp to feature; MODIFIER | silent_mutation | Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
vg0224219685 | C -> T | LOC_Os02g40000-LOC_Os02g40010 | intergenic_region ; MODIFIER | silent_mutation | Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
vg0224219685 | C -> DEL | N | N | silent_mutation | Average:34.059; most accessible tissue: Zhenshan97 panicle, score: 67.02 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0224219685 | 1.52E-06 | 1.52E-06 | mr1470 | Jap_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 |