| Variant ID: vg0816220261 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 16220261 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTTTTGCCAGGAATACAAATCTCTCAGTTCTTATGTTCTCTACTTCTGATCTACCTCAGCTCTTTGCCTTGCCACTTTCAGAGCAAGCTTTTCAGGAATA[C/T]
CTGGCAATGTCAGCTGCAGATCCCTTGGGGCATCTTAATGATGAGAGTGATCGCTGGACATATGTTTGGGGCAACGGTATTTTTTCCTCTCAGAAAATTT
AAATTTTCTGAGAGGAAAAAATACCGTTGCCCCAAACATATGTCCAGCGATCACTCTCATCATTAAGATGCCCCAAGGGATCTGCAGCTGACATTGCCAG[G/A]
TATTCCTGAAAAGCTTGCTCTGAAAGTGGCAAGGCAAAGAGCTGAGGTAGATCAGAAGTAGAGAACATAAGAACTGAGAGATTTGTATTCCTGGCAAAAG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.80% | 38.90% | 2.56% | 6.77% | NA |
| All Indica | 2759 | 77.00% | 19.10% | 3.23% | 0.62% | NA |
| All Japonica | 1512 | 5.20% | 74.60% | 1.19% | 18.98% | NA |
| Aus | 269 | 77.70% | 16.00% | 2.23% | 4.09% | NA |
| Indica I | 595 | 53.80% | 43.20% | 2.52% | 0.50% | NA |
| Indica II | 465 | 76.30% | 19.80% | 3.87% | 0.00% | NA |
| Indica III | 913 | 94.70% | 2.30% | 2.30% | 0.66% | NA |
| Indica Intermediate | 786 | 74.40% | 20.10% | 4.45% | 1.02% | NA |
| Temperate Japonica | 767 | 0.10% | 98.60% | 0.13% | 1.17% | NA |
| Tropical Japonica | 504 | 12.90% | 37.10% | 2.78% | 47.22% | NA |
| Japonica Intermediate | 241 | 5.40% | 76.80% | 1.24% | 16.60% | NA |
| VI/Aromatic | 96 | 7.30% | 91.70% | 0.00% | 1.04% | NA |
| Intermediate | 90 | 28.90% | 57.80% | 8.89% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0816220261 | C -> T | LOC_Os08g26685.1 | synonymous_variant ; p.Tyr85Tyr; LOW | synonymous_codon | Average:12.866; most accessible tissue: Callus, score: 40.693 | N | N | N | N |
| vg0816220261 | C -> DEL | LOC_Os08g26685.1 | N | frameshift_variant | Average:12.866; most accessible tissue: Callus, score: 40.693 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0816220261 | NA | 1.39E-06 | mr1029 | 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 |
| vg0816220261 | NA | 3.20E-06 | mr1047 | 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 |
| vg0816220261 | 6.05E-06 | 5.21E-07 | mr1189 | 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 |
| vg0816220261 | 2.72E-06 | 8.75E-07 | mr1471 | Ind_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 |
| vg0816220261 | 4.35E-07 | 4.88E-08 | mr1642 | Ind_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 |
| vg0816220261 | NA | 1.08E-10 | mr1722 | 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 |