| Variant ID: vg0217546819 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 17546819 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 245. )
TGTAGCATTTCACCCGAGAGTATTCCAATGGTATCGTATTTATTTTATCCCGTGGAAAGATCATATAGAGAGAACATTGACTAATAATTTATATATTACT[T/A]
GTGATAATCATATTCTAAGCAGGGGTTAAGATAATCTAAGGGTAGAGTGACACACAAGCATTAACTACTCATTCTCATAATATATCATCTAACCTAAGTG
CACTTAGGTTAGATGATATATTATGAGAATGAGTAGTTAATGCTTGTGTGTCACTCTACCCTTAGATTATCTTAACCCCTGCTTAGAATATGATTATCAC[A/T]
AGTAATATATAAATTATTAGTCAATGTTCTCTCTATATGATCTTTCCACGGGATAAAATAAATACGATACCATTGGAATACTCTCGGGTGAAATGCTACA
| 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 | 97.60% | 1.70% | 0.74% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 92.60% | 5.20% | 2.18% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 88.90% | 7.70% | 3.39% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 8.30% | 2.90% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0217546819 | T -> A | LOC_Os02g29520.1 | upstream_gene_variant ; 4629.0bp to feature; MODIFIER | silent_mutation | Average:57.33; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| vg0217546819 | T -> A | LOC_Os02g29520-LOC_Os02g29530 | intergenic_region ; MODIFIER | silent_mutation | Average:57.33; most accessible tissue: Zhenshan97 panicle, score: 81.135 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0217546819 | 7.92E-06 | NA | mr1202 | Jap_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 |
| vg0217546819 | 1.81E-06 | 1.81E-06 | mr1861 | 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 |