| Variant ID: vg0125082086 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 25082086 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAAAGATCGGCAAGCTGCTGGAATCCATCTAAGTACCTCGTAGATGCTCTAGGAGCCCTCCCCTAGCCATGTCTCACTCACATCACCCCGATCACCTTCA[C/T]
GGCTTAACTATGCCACTGCCGTCCTAGCCGTTAGCTCAACCACAAACCAAATTAACCCCTCCGCCGCCGCTCGCCGTCGCCGGAGAACCCTAGCTCCCTC
GAGGGAGCTAGGGTTCTCCGGCGACGGCGAGCGGCGGCGGAGGGGTTAATTTGGTTTGTGGTTGAGCTAACGGCTAGGACGGCAGTGGCATAGTTAAGCC[G/A]
TGAAGGTGATCGGGGTGATGTGAGTGAGACATGGCTAGGGGAGGGCTCCTAGAGCATCTACGAGGTACTTAGATGGATTCCAGCAGCTTGCCGATCTTTG
| 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 | 93.20% | 6.80% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 85.40% | 14.60% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 63.10% | 36.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 88.80% | 11.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 20.80% | 78.10% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 15.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0125082086 | C -> T | LOC_Os01g43774.1 | downstream_gene_variant ; 3537.0bp to feature; MODIFIER | silent_mutation | Average:52.339; most accessible tissue: Minghui63 root, score: 71.702 | N | N | N | N |
| vg0125082086 | C -> T | LOC_Os01g43774-LOC_Os01g43790 | intergenic_region ; MODIFIER | silent_mutation | Average:52.339; most accessible tissue: Minghui63 root, score: 71.702 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0125082086 | 4.12E-06 | NA | mr1104_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 |
| vg0125082086 | 2.41E-08 | NA | mr1155_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 |
| vg0125082086 | 5.19E-07 | NA | mr1155_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 |
| vg0125082086 | 3.85E-06 | NA | mr1226_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 |