| Variant ID: vg0519667518 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 19667518 |
| Reference Allele: A | Alternative Allele: G,T |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.91, G: 0.09, others allele: 0.00, population size: 65. )
GCGATCTTCCAGCAGCGATGGATCTCGGCAAGTCGGCTTCCACCAGCGCGACCCTGAAGAAGCTCCAAGAGGACGGCGCCCTTCCTGGCCGTGAAAAGGC[A/G,T]
GAGAGGGAAGCAGGAGGTACTAATCCTCAGCCCATCTTAGGTCGTATGGTTACGATCGAAGATTATGTTGTCTGCGGGTTTCTCCCTCCACCCTCCGAAT
ATTCGGAGGGTGGAGGGAGAAACCCGCAGACAACATAATCTTCGATCGTAACCATACGACCTAAGATGGGCTGAGGATTAGTACCTCCTGCTTCCCTCTC[T/C,A]
GCCTTTTCACGGCCAGGAAGGGCGCCGTCCTCTTGGAGCTTCTTCAGGGTCGCGCTGGTGGAAGCCGACTTGCCGAGATCCATCGCTGCTGGAAGATCGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.90% | 16.00% | 18.77% | 44.16% | T: 0.19% |
| All Indica | 2759 | 1.20% | 10.40% | 22.40% | 65.75% | T: 0.25% |
| All Japonica | 1512 | 61.80% | 26.30% | 2.18% | 9.72% | NA |
| Aus | 269 | 1.10% | 11.20% | 75.46% | 11.52% | T: 0.74% |
| Indica I | 595 | 1.00% | 2.70% | 10.59% | 85.71% | NA |
| Indica II | 465 | 1.50% | 12.50% | 24.30% | 61.72% | NA |
| Indica III | 913 | 1.00% | 15.60% | 29.46% | 53.56% | T: 0.44% |
| Indica Intermediate | 786 | 1.50% | 8.90% | 22.01% | 67.18% | T: 0.38% |
| Temperate Japonica | 767 | 92.40% | 0.70% | 2.48% | 4.43% | NA |
| Tropical Japonica | 504 | 8.30% | 74.40% | 0.60% | 16.67% | NA |
| Japonica Intermediate | 241 | 75.90% | 7.50% | 4.56% | 12.03% | NA |
| VI/Aromatic | 96 | 4.20% | 16.70% | 15.62% | 63.54% | NA |
| Intermediate | 90 | 15.60% | 26.70% | 20.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0519667518 | A -> T | LOC_Os05g33480.1 | synonymous_variant ; p.Ala28Ala; LOW | synonymous_codon | Average:18.234; most accessible tissue: Callus, score: 34.591 | N | N | N | N |
| vg0519667518 | A -> G | LOC_Os05g33480.1 | synonymous_variant ; p.Ala28Ala; LOW | synonymous_codon | Average:18.234; most accessible tissue: Callus, score: 34.591 | N | N | N | N |
| vg0519667518 | A -> G | LOC_Os05g33480.1 | synonymous_variant ; p.Ala28Ala; LOW | nonsynonymous_codon ; A28T | Average:18.234; most accessible tissue: Callus, score: 34.591 | unknown | unknown | DELETERIOUS | 0.04 |
| vg0519667518 | A -> G | LOC_Os05g33480.1 | synonymous_variant ; p.Ala28Ala; LOW | nonsynonymous_codon ; A28P | Average:18.234; most accessible tissue: Callus, score: 34.591 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0519667518 | A -> DEL | LOC_Os05g33480.1 | N | frameshift_variant | Average:18.234; most accessible tissue: Callus, score: 34.591 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0519667518 | NA | 5.46E-12 | mr1089 | Jap_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 |
| vg0519667518 | NA | 8.86E-12 | mr1093 | 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 |
| vg0519667518 | NA | 1.42E-08 | mr1129 | 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 |
| vg0519667518 | NA | 1.41E-10 | mr1235 | 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 |
| vg0519667518 | NA | 1.54E-10 | mr1251 | 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 |
| vg0519667518 | NA | 7.27E-06 | mr1271 | 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 |
| vg0519667518 | NA | 4.46E-07 | mr1271 | 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 |
| vg0519667518 | NA | 2.98E-06 | mr1422 | 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 |
| vg0519667518 | NA | 1.83E-11 | mr1435 | 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 |
| vg0519667518 | NA | 3.43E-06 | mr1443 | 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 |
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