| Variant ID: vg0604550200 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 4550200 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GGGGTCGGGCCCGAGGGTGACGTGGCCACCCCTCCCTCTGTCTCCCCGAGGGGTCGGGCCGCTCCCGTTTCGGCCCCGAGGCCTGGGACGCCCCGACCCC[C/T]
TATGGTTTTGGCGCCACGTGTGTGGGATAGGTGAGCCCAGCGGGGCTCACCTAACCGCATTTATAGCGGATTGGACGAGCGCGCCACGCCGCATTTAATG
CATTAAATGCGGCGTGGCGCGCTCGTCCAATCCGCTATAAATGCGGTTAGGTGAGCCCCGCTGGGCTCACCTATCCCACACACGTGGCGCCAAAACCATA[G/A]
GGGGTCGGGGCGTCCCAGGCCTCGGGGCCGAAACGGGAGCGGCCCGACCCCTCGGGGAGACAGAGGGAGGGGTGGCCACGTCACCCTCGGGCCCGACCCC
| 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 | 90.00% | 8.20% | 1.82% | 0.00% | NA |
| All Indica | 2759 | 96.60% | 0.70% | 2.72% | 0.00% | NA |
| All Japonica | 1512 | 75.80% | 23.60% | 0.60% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 83.00% | 2.40% | 14.62% | 0.00% | NA |
| Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.50% | 0.60% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 81.00% | 18.90% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 69.20% | 29.60% | 1.19% | 0.00% | NA |
| Japonica Intermediate | 241 | 73.00% | 26.10% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 94.80% | 5.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 6.70% | 2.22% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0604550200 | C -> T | LOC_Os06g09030.1 | upstream_gene_variant ; 3011.0bp to feature; MODIFIER | silent_mutation | Average:57.323; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 | N | N | N | N |
| vg0604550200 | C -> T | LOC_Os06g09040.1 | downstream_gene_variant ; 1677.0bp to feature; MODIFIER | silent_mutation | Average:57.323; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 | N | N | N | N |
| vg0604550200 | C -> T | LOC_Os06g09030-LOC_Os06g09040 | intergenic_region ; MODIFIER | silent_mutation | Average:57.323; most accessible tissue: Zhenshan97 flag leaf, score: 78.0 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0604550200 | NA | 1.52E-06 | mr1636 | 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 |
| vg0604550200 | NA | 2.54E-06 | mr1766 | 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 |
| vg0604550200 | 1.29E-09 | NA | mr1137_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 |
| vg0604550200 | 3.89E-07 | NA | mr1137_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 |