| Variant ID: vg0420619843 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20619843 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAATAGAGCTCTCATCGATCAGAAAAAAGGGGAAAAAGAAGTCCACTAGAGCTCTAGATATATACTCCCTCTATCCAAAATATAATTATTTTTAAACTTT[A/G]
ACACGGTCTTCGAGATGTTATTTTGACCAACAATATCTATGTTTTAAATAAAAAGAGTTAGATATTATGATAGTTTGTTTAATGATAAATTTAGAAACAT
ATGTTTCTAAATTTATCATTAAACAAACTATCATAATATCTAACTCTTTTTATTTAAAACATAGATATTGTTGGTCAAAATAACATCTCGAAGACCGTGT[T/C]
AAAGTTTAAAAATAATTATATTTTGGATAGAGGGAGTATATATCTAGAGCTCTAGTGGACTTCTTTTTCCCCTTTTTTCTGATCGATGAGAGCTCTATTT
| 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 | 84.80% | 15.10% | 0.06% | 0.00% | NA |
| All Indica | 2759 | 98.90% | 1.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 56.00% | 44.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.00% | 0.90% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 59.30% | 40.70% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 57.90% | 42.10% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 41.10% | 58.50% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 77.80% | 21.10% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420619843 | A -> G | LOC_Os04g34050.1 | upstream_gene_variant ; 4755.0bp to feature; MODIFIER | silent_mutation | Average:42.784; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| vg0420619843 | A -> G | LOC_Os04g34040.1 | intron_variant ; MODIFIER | silent_mutation | Average:42.784; most accessible tissue: Zhenshan97 panicle, score: 61.671 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0420619843 | 3.18E-06 | NA | mr1092 | 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 |
| vg0420619843 | NA | 3.02E-06 | mr1092 | 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 |
| vg0420619843 | NA | 5.09E-06 | mr1619 | 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 |