| Variant ID: vg0220752536 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20752536 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACGTCAAGGAAGACGAAAAGCGGCGGAGGATCCGACGGAGAAGGCGACGTGGGCGAGGTTGACGGGAGAGAGGAGGCAGCGCGGGTGAGGTTGGCGGGGG[G/A]
AGGCGGGAGGAAGCAGCGTGGGCGAGGGAGCTCGTGGAAGAGGAGGCGGCATCGACGGGGAGAGGAGGCGACGTGAGCGAGGGAGCGTGCCCGATATTTT
AAAATATCGGGCACGCTCCCTCGCTCACGTCGCCTCCTCTCCCCGTCGATGCCGCCTCCTCTTCCACGAGCTCCCTCGCCCACGCTGCTTCCTCCCGCCT[C/T]
CCCCCGCCAACCTCACCCGCGCTGCCTCCTCTCTCCCGTCAACCTCGCCCACGTCGCCTTCTCCGTCGGATCCTCCGCCGCTTTTCGTCTTCCTTGACGT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 82.80% | 3.80% | 8.74% | 4.63% | NA |
| All Indica | 2759 | 77.40% | 0.30% | 14.46% | 7.79% | NA |
| All Japonica | 1512 | 88.00% | 11.30% | 0.53% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 60.00% | 0.00% | 33.61% | 6.39% | NA |
| Indica II | 465 | 83.20% | 0.60% | 11.18% | 4.95% | NA |
| Indica III | 913 | 87.00% | 0.00% | 4.93% | 8.11% | NA |
| Indica Intermediate | 786 | 76.10% | 0.80% | 12.98% | 10.18% | NA |
| Temperate Japonica | 767 | 77.20% | 21.90% | 0.78% | 0.13% | NA |
| Tropical Japonica | 504 | 99.40% | 0.40% | 0.00% | 0.20% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.40% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 1.10% | 6.67% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0220752536 | G -> A | LOC_Os02g34600.1 | upstream_gene_variant ; 1157.0bp to feature; MODIFIER | silent_mutation | Average:72.257; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
| vg0220752536 | G -> A | LOC_Os02g34600.2 | upstream_gene_variant ; 1157.0bp to feature; MODIFIER | silent_mutation | Average:72.257; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
| vg0220752536 | G -> A | LOC_Os02g34610.1 | downstream_gene_variant ; 372.0bp to feature; MODIFIER | silent_mutation | Average:72.257; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
| vg0220752536 | G -> A | LOC_Os02g34600-LOC_Os02g34610 | intergenic_region ; MODIFIER | silent_mutation | Average:72.257; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
| vg0220752536 | G -> DEL | N | N | silent_mutation | Average:72.257; most accessible tissue: Zhenshan97 young leaf, score: 86.542 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220752536 | 4.03E-07 | 4.03E-07 | mr1499_2 | 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 |
| vg0220752536 | 1.73E-06 | 2.29E-08 | mr1576_2 | 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 |
| vg0220752536 | NA | 6.61E-06 | mr1627_2 | 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 |