| Variant ID: vg0128078547 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28078547 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.96, C: 0.04, others allele: 0.00, population size: 93. )
TCATATTTCAGACAGTACAAAAATACAGGCTCAGAAAGCAGTATAATCATTTCTAAGAGTCTGAATTGTTGTAGTATTATTAACAAAATTAACAAGCAGT[A/C]
CGTGCTAATGAAGTGCTGCAGTGCCATTGAGTTAGATCAGCTCTGCACACTGTTGGCGGAAATGTCAACTTGTAATCTCGGAAAAAACAGCCATGCAACC
GGTTGCATGGCTGTTTTTTCCGAGATTACAAGTTGACATTTCCGCCAACAGTGTGCAGAGCTGATCTAACTCAATGGCACTGCAGCACTTCATTAGCACG[T/G]
ACTGCTTGTTAATTTTGTTAATAATACTACAACAATTCAGACTCTTAGAAATGATTATACTGCTTTCTGAGCCTGTATTTTTGTACTGTCTGAAATATGA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 90.10% | 2.70% | 5.04% | 2.18% | NA |
| All Indica | 2759 | 85.80% | 2.10% | 8.37% | 3.70% | NA |
| All Japonica | 1512 | 95.60% | 4.20% | 0.13% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 85.70% | 1.20% | 9.24% | 3.87% | NA |
| Indica II | 465 | 70.80% | 3.40% | 17.20% | 8.60% | NA |
| Indica III | 913 | 96.50% | 0.90% | 2.19% | 0.44% | NA |
| Indica Intermediate | 786 | 82.30% | 3.60% | 9.67% | 4.45% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 87.90% | 11.70% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 3.30% | 5.56% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128078547 | A -> DEL | N | N | silent_mutation | Average:18.399; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128078547 | A -> C | LOC_Os01g48920.1 | upstream_gene_variant ; 2119.0bp to feature; MODIFIER | silent_mutation | Average:18.399; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128078547 | A -> C | LOC_Os01g48930.1 | upstream_gene_variant ; 1845.0bp to feature; MODIFIER | silent_mutation | Average:18.399; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128078547 | A -> C | LOC_Os01g48930.2 | upstream_gene_variant ; 1845.0bp to feature; MODIFIER | silent_mutation | Average:18.399; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128078547 | A -> C | LOC_Os01g48920-LOC_Os01g48930 | intergenic_region ; MODIFIER | silent_mutation | Average:18.399; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0128078547 | NA | 7.53E-06 | mr1045 | 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 |
| vg0128078547 | 3.15E-06 | 3.14E-06 | mr1628 | 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 |
| vg0128078547 | 2.85E-06 | 2.85E-06 | mr1784 | 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 |