| Variant ID: vg0608860704 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 8860704 |
| 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: 73. )
AACGGCAAATGGCGCATGTGTATAGATTTCACGGACCTGAACAAAGCATGTCCAAAGGACGATTTCCCTTTGCCGCGGATCGATCAGCTCGTGGATTCAA[C/T]
AGCTGGCTGCGAACTCATGAGTTTCCTGGACGCATATTCCGGCTATCACTAGATCCATATGAATCCGCCTGACATCCCGAAGACAGCCTTCATCACCCCG
CGGGGTGATGAAGGCTGTCTTCGGGATGTCAGGCGGATTCATATGGATCTAGTGATAGCCGGAATATGCGTCCAGGAAACTCATGAGTTCGCAGCCAGCT[G/A]
TTGAATCCACGAGCTGATCGATCCGCGGCAAAGGGAAATCGTCCTTTGGACATGCTTTGTTCAGGTCCGTGAAATCTATACACATGCGCCATTTGCCGTT
| 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 | 68.70% | 14.60% | 2.24% | 14.41% | NA |
| All Indica | 2759 | 81.00% | 18.00% | 0.80% | 0.14% | NA |
| All Japonica | 1512 | 43.50% | 11.40% | 3.24% | 41.93% | NA |
| Aus | 269 | 94.10% | 2.60% | 2.97% | 0.37% | NA |
| Indica I | 595 | 94.30% | 3.50% | 1.85% | 0.34% | NA |
| Indica II | 465 | 80.20% | 19.40% | 0.43% | 0.00% | NA |
| Indica III | 913 | 69.40% | 30.20% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 85.00% | 14.00% | 0.89% | 0.13% | NA |
| Temperate Japonica | 767 | 74.60% | 0.00% | 1.69% | 23.73% | NA |
| Tropical Japonica | 504 | 9.10% | 30.20% | 5.16% | 55.56% | NA |
| Japonica Intermediate | 241 | 16.20% | 8.30% | 4.15% | 71.37% | NA |
| VI/Aromatic | 96 | 39.60% | 2.10% | 20.83% | 37.50% | NA |
| Intermediate | 90 | 72.20% | 13.30% | 7.78% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0608860704 | C -> T | LOC_Os06g15650.1 | upstream_gene_variant ; 4632.0bp to feature; MODIFIER | silent_mutation | Average:39.697; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0608860704 | C -> T | LOC_Os06g15640.1 | intron_variant ; MODIFIER | silent_mutation | Average:39.697; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0608860704 | C -> DEL | N | N | silent_mutation | Average:39.697; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0608860704 | NA | 3.30E-08 | mr1217 | 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 |
| vg0608860704 | NA | 1.09E-06 | mr1227 | 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 |
| vg0608860704 | 3.66E-07 | 2.46E-09 | mr1439 | 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 |
| vg0608860704 | NA | 2.07E-07 | mr1845 | 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 |
| vg0608860704 | NA | 6.39E-06 | mr1852 | 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 |