| Variant ID: vg0408074000 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 8074000 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 122. )
GTGCACGATGCGAGACGTGGGGTGGGATCGGAAGCAGTGGAGTTGTTTTTATTATCGAAGTAAATTGTTTACTCGAATAAAGGTGGGTGGTTGAGGCGCG[C/T]
GATAGGAGTAAATCGTTTATTCCGACAATGGTAAGAGTGGGATGACGGGACGTGAGGTGGGGGGGGCCTGGGCTGGTGCATGTTTGGCGCGCTGCGCTCC
GGAGCGCAGCGCGCCAAACATGCACCAGCCCAGGCCCCCCCCACCTCACGTCCCGTCATCCCACTCTTACCATTGTCGGAATAAACGATTTACTCCTATC[G/A]
CGCGCCTCAACCACCCACCTTTATTCGAGTAAACAATTTACTTCGATAATAAAAACAACTCCACTGCTTCCGATCCCACCCCACGTCTCGCATCGTGCAC
| 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 | 58.90% | 24.90% | 4.13% | 12.04% | NA |
| All Indica | 2759 | 89.70% | 7.30% | 2.32% | 0.72% | NA |
| All Japonica | 1512 | 3.30% | 62.20% | 3.24% | 31.28% | NA |
| Aus | 269 | 65.40% | 2.20% | 18.59% | 13.75% | NA |
| Indica I | 595 | 96.80% | 1.50% | 1.18% | 0.50% | NA |
| Indica II | 465 | 70.10% | 25.80% | 2.37% | 1.72% | NA |
| Indica III | 913 | 94.50% | 3.50% | 1.75% | 0.22% | NA |
| Indica Intermediate | 786 | 90.20% | 5.10% | 3.82% | 0.89% | NA |
| Temperate Japonica | 767 | 0.10% | 96.00% | 0.65% | 3.26% | NA |
| Tropical Japonica | 504 | 8.30% | 7.50% | 6.94% | 77.18% | NA |
| Japonica Intermediate | 241 | 2.90% | 68.90% | 3.73% | 24.48% | NA |
| VI/Aromatic | 96 | 41.70% | 3.10% | 27.08% | 28.12% | NA |
| Intermediate | 90 | 48.90% | 31.10% | 6.67% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0408074000 | C -> DEL | N | N | silent_mutation | Average:32.031; most accessible tissue: Callus, score: 50.784 | N | N | N | N |
| vg0408074000 | C -> T | LOC_Os04g14410.1 | upstream_gene_variant ; 1716.0bp to feature; MODIFIER | silent_mutation | Average:32.031; most accessible tissue: Callus, score: 50.784 | N | N | N | N |
| vg0408074000 | C -> T | LOC_Os04g14420.1 | upstream_gene_variant ; 3757.0bp to feature; MODIFIER | silent_mutation | Average:32.031; most accessible tissue: Callus, score: 50.784 | N | N | N | N |
| vg0408074000 | C -> T | LOC_Os04g14410-LOC_Os04g14420 | intergenic_region ; MODIFIER | silent_mutation | Average:32.031; most accessible tissue: Callus, score: 50.784 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0408074000 | NA | 1.17E-07 | mr1993 | 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 |
| vg0408074000 | NA | 2.08E-06 | mr1668_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 |
| vg0408074000 | 1.51E-06 | NA | mr1836_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 |