| Variant ID: vg1216568438 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 16568438 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAAAAACTATCGAAAAAACACGCCATTTATAAAAAAATGGTTTTTAAAAACCGTGCAAGAAAAAAACACCGTCTATTAAAAAAATCGCCCTGAAAAAACT[G/A]
TCAGAAAAAAGCTAAATTGATGGACGCTTCAGTCGGATAGGATCCATCGATTTTTTGCCATCTACTACATGGCTTTATTTTGTCATATATTCTCCTGTAT
ATACAGGAGAATATATGACAAAATAAAGCCATGTAGTAGATGGCAAAAAATCGATGGATCCTATCCGACTGAAGCGTCCATCAATTTAGCTTTTTTCTGA[C/T]
AGTTTTTTCAGGGCGATTTTTTTAATAGACGGTGTTTTTTTCTTGCACGGTTTTTAAAAACCATTTTTTTATAAATGGCGTGTTTTTTCGATAGTTTTTT
| 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 | 75.60% | 2.30% | 2.56% | 19.59% | NA |
| All Indica | 2759 | 72.30% | 0.30% | 1.01% | 26.39% | NA |
| All Japonica | 1512 | 89.30% | 5.60% | 2.98% | 2.18% | NA |
| Aus | 269 | 26.00% | 5.20% | 14.50% | 54.28% | NA |
| Indica I | 595 | 88.60% | 0.20% | 0.00% | 11.26% | NA |
| Indica II | 465 | 83.90% | 0.20% | 1.72% | 14.19% | NA |
| Indica III | 913 | 52.60% | 0.00% | 0.99% | 46.44% | NA |
| Indica Intermediate | 786 | 76.20% | 0.60% | 1.40% | 21.76% | NA |
| Temperate Japonica | 767 | 92.60% | 5.50% | 1.69% | 0.26% | NA |
| Tropical Japonica | 504 | 86.30% | 4.00% | 3.97% | 5.75% | NA |
| Japonica Intermediate | 241 | 85.10% | 9.10% | 4.98% | 0.83% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 4.17% | 6.25% | NA |
| Intermediate | 90 | 76.70% | 3.30% | 5.56% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1216568438 | G -> DEL | N | N | silent_mutation | Average:8.47; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1216568438 | G -> A | LOC_Os12g28065.1 | upstream_gene_variant ; 2496.0bp to feature; MODIFIER | silent_mutation | Average:8.47; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1216568438 | G -> A | LOC_Os12g28070.1 | downstream_gene_variant ; 3497.0bp to feature; MODIFIER | silent_mutation | Average:8.47; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1216568438 | G -> A | LOC_Os12g28065-LOC_Os12g28070 | intergenic_region ; MODIFIER | silent_mutation | Average:8.47; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1216568438 | 3.21E-06 | 2.21E-07 | mr1071_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 |
| vg1216568438 | NA | 9.70E-06 | mr1080_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 |
| vg1216568438 | NA | 3.55E-06 | mr1203_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 |
| vg1216568438 | 7.65E-08 | 1.21E-07 | mr1613_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 |
| vg1216568438 | 1.06E-07 | 4.59E-07 | mr1795_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 |
| vg1216568438 | NA | 4.69E-06 | mr1913_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 |