| Variant ID: vg0111823078 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 11823078 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 107. )
TCTCTAGGGACAACCATCTTTTTCCTTAACACACCGAACTTCATATTGCGACCGGTTGGACTTGGCAACCCAAAACTCTCTATGAAGTGACACTGCAAAA[C/T]
GTTTTACCTCCTCCTTCATATCTTCTGCTCTAGTATAAATCGCTCCCTGAATAACCTCATTTTCTTTGTACTCCCATCTCACACTATCCTCTTCAGAGAC
GTCTCTGAAGAGGATAGTGTGAGATGGGAGTACAAAGAAAATGAGGTTATTCAGGGAGCGATTTATACTAGAGCAGAAGATATGAAGGAGGAGGTAAAAC[G/A]
TTTTGCAGTGTCACTTCATAGAGAGTTTTGGGTTGCCAAGTCCAACCGGTCGCAATATGAAGTTCGGTGTGTTAAGGAAAAAGATGGTTGTCCCTAGAGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.30% | 1.90% | 18.28% | 45.47% | NA |
| All Indica | 2759 | 3.00% | 3.20% | 29.97% | 63.79% | NA |
| All Japonica | 1512 | 96.20% | 0.00% | 0.40% | 3.44% | NA |
| Aus | 269 | 8.90% | 0.40% | 7.06% | 83.64% | NA |
| Indica I | 595 | 2.40% | 2.50% | 18.49% | 76.64% | NA |
| Indica II | 465 | 4.50% | 1.10% | 12.69% | 81.72% | NA |
| Indica III | 913 | 1.90% | 4.90% | 46.00% | 47.21% | NA |
| Indica Intermediate | 786 | 3.90% | 3.10% | 30.28% | 62.72% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.52% | 1.69% | NA |
| Tropical Japonica | 504 | 93.30% | 0.00% | 0.40% | 6.35% | NA |
| Japonica Intermediate | 241 | 97.10% | 0.00% | 0.00% | 2.90% | NA |
| VI/Aromatic | 96 | 21.90% | 0.00% | 1.04% | 77.08% | NA |
| Intermediate | 90 | 43.30% | 2.20% | 12.22% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0111823078 | C -> T | LOC_Os01g21190.1 | splice_region_variant&intron_variant ; LOW | silent_mutation | Average:11.684; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0111823078 | C -> T | LOC_Os01g21200.1 | downstream_gene_variant ; 2084.0bp to feature; MODIFIER | silent_mutation | Average:11.684; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| vg0111823078 | C -> DEL | N | N | silent_mutation | Average:11.684; most accessible tissue: Minghui63 root, score: 19.68 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0111823078 | NA | 1.13E-82 | mr1672 | 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 |
| vg0111823078 | NA | 1.37E-89 | mr1758 | 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 |
| vg0111823078 | NA | 1.91E-20 | mr1838 | 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 |
| vg0111823078 | NA | 1.11E-07 | mr1335_2 | 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 |
| vg0111823078 | NA | 9.39E-63 | mr1733_2 | 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 |
| vg0111823078 | 2.91E-07 | NA | mr1758_2 | 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 |