| Variant ID: vg0616941958 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 16941958 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )
ATTCCAACAATCTCATTCACTGTAGCTTGTTGGTACCAAGACTGAAGAAGGCGCGGGACAAGCAGTATTTATAAAGCTTAGCTATTGGTTGAAATTAAGG[C/T]
GACAATGTGGCTATTGCCTGAAGTGAAAAGTGAAAACTGAATTGGCTAGCAGAGAGTGCAGTGGAGTTGGTAACGATCTTGCGAGCTATGCTTGATTCTG
CAGAATCAAGCATAGCTCGCAAGATCGTTACCAACTCCACTGCACTCTCTGCTAGCCAATTCAGTTTTCACTTTTCACTTCAGGCAATAGCCACATTGTC[G/A]
CCTTAATTTCAACCAATAGCTAAGCTTTATAAATACTGCTTGTCCCGCGCCTTCTTCAGTCTTGGTACCAACAAGCTACAGTGAATGAGATTGTTGGAAT
| 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 | 95.80% | 3.80% | 0.42% | 0.00% | NA |
| All Indica | 2759 | 93.20% | 6.10% | 0.69% | 0.00% | NA |
| All Japonica | 1512 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.00% | 0.34% | 0.00% | NA |
| Indica II | 465 | 94.60% | 4.30% | 1.08% | 0.00% | NA |
| Indica III | 913 | 92.60% | 7.20% | 0.22% | 0.00% | NA |
| Indica Intermediate | 786 | 89.10% | 9.70% | 1.27% | 0.00% | NA |
| Temperate Japonica | 767 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 5.60% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0616941958 | C -> T | LOC_Os06g29570.1 | downstream_gene_variant ; 686.0bp to feature; MODIFIER | silent_mutation | Average:33.557; most accessible tissue: Callus, score: 57.291 | N | N | N | N |
| vg0616941958 | C -> T | LOC_Os06g29570-LOC_Os06g29580 | intergenic_region ; MODIFIER | silent_mutation | Average:33.557; most accessible tissue: Callus, score: 57.291 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0616941958 | 7.82E-06 | NA | mr1003 | 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 |
| vg0616941958 | NA | 4.25E-07 | mr1003 | 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 |
| vg0616941958 | NA | 8.95E-07 | mr1530_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 |