| Variant ID: vg0612260128 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 12260128 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATATACTATGAGAAGTATATAAACCAGTAGTAAAGTGGAGAGGCCTCCAAAGATTTTATGCAAGAACAACATTTCAAACTACCGTGCCAATTTCTCCTA[C/T]
ATAAATTGTCCTTTATTAAAACAACCATTTAGGTACGTACCACATAAAAATCTTGATCTTAAGAGGTATCTTAAGTTTTCATATAATATTTTTTCTCTCA
TGAGAGAAAAAATATTATATGAAAACTTAAGATACCTCTTAAGATCAAGATTTTTATGTGGTACGTACCTAAATGGTTGTTTTAATAAAGGACAATTTAT[G/A]
TAGGAGAAATTGGCACGGTAGTTTGAAATGTTGTTCTTGCATAAAATCTTTGGAGGCCTCTCCACTTTACTACTGGTTTATATACTTCTCATAGTATATC
| 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 | 96.10% | 3.70% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 98.70% | 1.10% | 0.22% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 48.30% | 51.30% | 0.37% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 96.30% | 3.00% | 0.65% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.10% | 1.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0612260128 | C -> T | LOC_Os06g21220.1 | upstream_gene_variant ; 1262.0bp to feature; MODIFIER | silent_mutation | Average:30.624; most accessible tissue: Zhenshan97 young leaf, score: 53.314 | N | N | N | N |
| vg0612260128 | C -> T | LOC_Os06g21210-LOC_Os06g21220 | intergenic_region ; MODIFIER | silent_mutation | Average:30.624; most accessible tissue: Zhenshan97 young leaf, score: 53.314 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0612260128 | 8.15E-07 | NA | mr1695 | 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 |
| vg0612260128 | NA | 1.58E-06 | mr1931 | 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 |
| vg0612260128 | 1.77E-06 | NA | mr1695_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 |