| Variant ID: vg0114526997 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14526997 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.68, C: 0.33, others allele: 0.00, population size: 209. )
CTGGCGAAAAAGGTTACTATCATGTGCGGATTGCATATTTCCAAGTCTTTGGCTTCATTAATTTTGGCCCTGGTCACAGATGATGATGTTGGAAGACATA[C/T]
GTATAAGTTAATGTACCATGAAAAATATAAATCTATATATAGGCATTACACAAAAAGTATCATAGTATATATCTTGAGTAGGGAACTATTACAAACTAAT
ATTAGTTTGTAATAGTTCCCTACTCAAGATATATACTATGATACTTTTTGTGTAATGCCTATATATAGATTTATATTTTTCATGGTACATTAACTTATAC[G/A]
TATGTCTTCCAACATCATCATCTGTGACCAGGGCCAAAATTAATGAAGCCAAAGACTTGGAAATATGCAATCCGCACATGATAGTAACCTTTTTCGCCAG
| 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 | 81.70% | 14.10% | 0.30% | 3.87% | NA |
| All Indica | 2759 | 71.70% | 21.30% | 0.51% | 6.49% | NA |
| All Japonica | 1512 | 97.50% | 2.40% | 0.00% | 0.07% | NA |
| Aus | 269 | 86.20% | 13.00% | 0.00% | 0.74% | NA |
| Indica I | 595 | 85.50% | 9.60% | 0.34% | 4.54% | NA |
| Indica II | 465 | 81.50% | 15.70% | 0.22% | 2.58% | NA |
| Indica III | 913 | 59.80% | 32.00% | 0.11% | 8.11% | NA |
| Indica Intermediate | 786 | 69.30% | 21.00% | 1.27% | 8.40% | NA |
| Temperate Japonica | 767 | 98.70% | 1.20% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 95.00% | 5.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 90.00% | 8.90% | 0.00% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114526997 | C -> T | LOC_Os01g25630.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.022; most accessible tissue: Callus, score: 80.0 | N | N | N | N |
| vg0114526997 | C -> DEL | N | N | silent_mutation | Average:48.022; most accessible tissue: Callus, score: 80.0 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0114526997 | NA | 9.14E-06 | mr1125 | Ind_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 |
| vg0114526997 | NA | 1.28E-07 | mr1458 | Ind_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 |
| vg0114526997 | NA | 5.94E-08 | mr1458_2 | Ind_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 |