| Variant ID: vg0628359678 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 28359678 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATTAGATGTAAAAATTAAAACATCATTTATAATCAACCTAATATATAGTTCACTCACATATTAGTTAGCTATAAATATATATTTCATTATACCTAATTCT[C/T]
CCGTCTATTTTGTATAGTTCATTAAAATATATATTTCATTATACCTAATTCTCCCGTCTATTTTGTATAGTTCATTAGTAGAGATTATTTTGCAGTTGGC
GCCAACTGCAAAATAATCTCTACTAATGAACTATACAAAATAGACGGGAGAATTAGGTATAATGAAATATATATTTTAATGAACTATACAAAATAGACGG[G/A]
AGAATTAGGTATAATGAAATATATATTTATAGCTAACTAATATGTGAGTGAACTATATATTAGGTTGATTATAAATGATGTTTTAATTTTTACATCTAAT
| 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 | 87.80% | 12.00% | 0.15% | 0.00% | NA |
| All Indica | 2759 | 83.60% | 16.10% | 0.25% | 0.00% | NA |
| All Japonica | 1512 | 97.20% | 2.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 72.90% | 27.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 89.90% | 10.10% | 0.00% | 0.00% | NA |
| Indica III | 913 | 72.00% | 27.70% | 0.33% | 0.00% | NA |
| Indica Intermediate | 786 | 82.10% | 17.40% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.30% | 7.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 94.40% | 5.60% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0628359678 | C -> T | LOC_Os06g46680.1 | downstream_gene_variant ; 1278.0bp to feature; MODIFIER | silent_mutation | Average:31.905; most accessible tissue: Callus, score: 67.921 | N | N | N | N |
| vg0628359678 | C -> T | LOC_Os06g46690.1 | downstream_gene_variant ; 3953.0bp to feature; MODIFIER | silent_mutation | Average:31.905; most accessible tissue: Callus, score: 67.921 | N | N | N | N |
| vg0628359678 | C -> T | LOC_Os06g46680-LOC_Os06g46690 | intergenic_region ; MODIFIER | silent_mutation | Average:31.905; most accessible tissue: Callus, score: 67.921 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0628359678 | NA | 2.28E-10 | Heading_date | Ind_All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0628359678 | 6.19E-07 | 6.18E-07 | mr1643_2 | 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 |
| vg0628359678 | NA | 1.96E-06 | mr1943_2 | 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 |