| Variant ID: vg0913504506 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 13504506 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGCTGTCGTGCTGTTTTCAGGCTGACGGTCAGACCGCGAGAGGACCTGCGGTTAGACCGGTTAGAGTTCGGTCAGACCGATCCTAGTAGGTCGGATAGAC[C/T]
GCCAAACGTGTGTTCCATTGGCTTTTGAGGTTTGTCGAAACAAGATTTCGGCAATACTAAAAGGGGGTGGCTATCAAGCTAGAAAAGTGGATGGGTTTGA
TCAAACCCATCCACTTTTCTAGCTTGATAGCCACCCCCTTTTAGTATTGCCGAAATCTTGTTTCGACAAACCTCAAAAGCCAATGGAACACACGTTTGGC[G/A]
GTCTATCCGACCTACTAGGATCGGTCTGACCGAACTCTAACCGGTCTAACCGCAGGTCCTCTCGCGGTCTGACCGTCAGCCTGAAAACAGCACGACAGCG
| 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 | 56.50% | 38.90% | 4.59% | 0.02% | NA |
| All Indica | 2759 | 82.90% | 12.50% | 4.57% | 0.00% | NA |
| All Japonica | 1512 | 3.80% | 92.60% | 3.51% | 0.07% | NA |
| Aus | 269 | 75.80% | 15.60% | 8.55% | 0.00% | NA |
| Indica I | 595 | 77.60% | 18.00% | 4.37% | 0.00% | NA |
| Indica II | 465 | 77.00% | 15.30% | 7.74% | 0.00% | NA |
| Indica III | 913 | 90.60% | 7.20% | 2.19% | 0.00% | NA |
| Indica Intermediate | 786 | 81.40% | 13.00% | 5.60% | 0.00% | NA |
| Temperate Japonica | 767 | 3.70% | 95.40% | 0.91% | 0.00% | NA |
| Tropical Japonica | 504 | 4.40% | 87.10% | 8.33% | 0.20% | NA |
| Japonica Intermediate | 241 | 3.30% | 95.00% | 1.66% | 0.00% | NA |
| VI/Aromatic | 96 | 84.40% | 8.30% | 7.29% | 0.00% | NA |
| Intermediate | 90 | 42.20% | 48.90% | 8.89% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0913504506 | C -> DEL | N | N | silent_mutation | Average:34.812; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| vg0913504506 | C -> T | LOC_Os09g22350.1 | upstream_gene_variant ; 1492.0bp to feature; MODIFIER | silent_mutation | Average:34.812; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| vg0913504506 | C -> T | LOC_Os09g22360.1 | downstream_gene_variant ; 4734.0bp to feature; MODIFIER | silent_mutation | Average:34.812; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| vg0913504506 | C -> T | LOC_Os09g22340-LOC_Os09g22350 | intergenic_region ; MODIFIER | silent_mutation | Average:34.812; most accessible tissue: Minghui63 panicle, score: 70.194 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0913504506 | NA | 5.26E-26 | mr1024 | 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 |
| vg0913504506 | 3.01E-06 | 5.84E-06 | mr1712 | 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 |
| vg0913504506 | NA | 4.92E-18 | mr1715 | 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 |