| Variant ID: vg0140047043 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 40047043 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 103. )
CTCACCCAGAGTCCCCGGCCGAACCGGCAAAGGGGGGCCAGCGCGGTCTCCCGGTGAGGAGCCCCACGCTCCGTCACGGTGTCAGTATCATGAGCCTCTC[G/A]
CCGTTGAGCTCTTGAGATTCGGCGCGGCGGAGGAAATGTCGAGGTGAACCCAACTATCATATCATTCGCAGTTGAGGCATTCAATTGCCGTCGAGGTAGC
GCTACCTCGACGGCAATTGAATGCCTCAACTGCGAATGATATGATAGTTGGGTTCACCTCGACATTTCCTCCGCCGCGCCGAATCTCAAGAGCTCAACGG[C/T]
GAGAGGCTCATGATACTGACACCGTGACGGAGCGTGGGGCTCCTCACCGGGAGACCGCGCTGGCCCCCCTTTGCCGGTTCGGCCGGGGACTCTGGGTGAG
| 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 | 94.90% | 4.80% | 0.30% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.20% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 84.90% | 14.40% | 0.73% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.50% | 0.40% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 78.00% | 20.60% | 1.43% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 78.00% | 22.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0140047043 | G -> A | LOC_Os01g68920.1 | downstream_gene_variant ; 2791.0bp to feature; MODIFIER | silent_mutation | Average:47.911; most accessible tissue: Callus, score: 82.025 | N | N | N | N |
| vg0140047043 | G -> A | LOC_Os01g68920-LOC_Os01g68930 | intergenic_region ; MODIFIER | silent_mutation | Average:47.911; most accessible tissue: Callus, score: 82.025 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0140047043 | NA | 5.21E-06 | mr1154 | 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 |
| vg0140047043 | 5.27E-06 | 4.25E-08 | mr1092_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 |
| vg0140047043 | NA | 1.84E-06 | mr1154_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 |