| Variant ID: vg0616984615 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 16984615 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TTTCGTGGCGGCTATTTTGGGTTTTCGCTAGTGGAATTTAGAGCAGCCACAAAGTAAAGGCCAGTGAAGATCAAGATCTTCGCTAGCGGTTATCAACCGC[C/T]
AGCGATAATTCATCTTCGCTGGCTGTCGTCTTAAGCTAGCTGCCAGCAAAGATCCATTTTCGCTGGTGGTTGGCTTAAGACGGCTGCCAGCGAATTTTTT
AAAAAATTCGCTGGCAGCCGTCTTAAGCCAACCACCAGCGAAAATGGATCTTTGCTGGCAGCTAGCTTAAGACGACAGCCAGCGAAGATGAATTATCGCT[G/A]
GCGGTTGATAACCGCTAGCGAAGATCTTGATCTTCACTGGCCTTTACTTTGTGGCTGCTCTAAATTCCACTAGCGAAAACCCAAAATAGCCGCCACGAAA
| 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 | 97.30% | 2.10% | 0.63% | 0.00% | NA |
| All Indica | 2759 | 99.40% | 0.50% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 92.60% | 5.60% | 1.79% | 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 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 1.10% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 97.90% | 1.20% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 83.50% | 13.30% | 3.17% | 0.00% | NA |
| Japonica Intermediate | 241 | 94.60% | 3.70% | 1.66% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0616984615 | C -> T | LOC_Os06g29620.1 | upstream_gene_variant ; 459.0bp to feature; MODIFIER | silent_mutation | Average:54.413; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |
| vg0616984615 | C -> T | LOC_Os06g29620-LOC_Os06g29630 | intergenic_region ; MODIFIER | silent_mutation | Average:54.413; most accessible tissue: Zhenshan97 panicle, score: 75.67 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0616984615 | NA | 1.64E-08 | mr1951 | 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 |
| vg0616984615 | NA | 2.95E-06 | mr1236_2 | 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 |
| vg0616984615 | NA | 2.94E-15 | mr1769_2 | 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 |
| vg0616984615 | 2.95E-06 | 7.06E-08 | mr1951_2 | 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 |