| Variant ID: vg0137140050 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37140050 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CGTAGTATTAGAATATATCGCATTCAATCAAATTTTCTTATATATTAAAACAGATAAGTACTCCTTGTCCCAAAATATAAGCATTTTTAGAATAGTGCCA[A/G]
GTCAAATACTTTAAACGTTGGCTATTAATAACAAAAAAAAAAATCAATCATGTAAAATTGATGTCACTAGATTTATTATTAAACAAACTATTCTAACATG
CATGTTAGAATAGTTTGTTTAATAATAAATCTAGTGACATCAATTTTACATGATTGATTTTTTTTTTTGTTATTAATAGCCAACGTTTAAAGTATTTGAC[T/C]
TGGCACTATTCTAAAAATGCTTATATTTTGGGACAAGGAGTACTTATCTGTTTTAATATATAAGAAAATTTGATTGAATGCGATATATTCTAATACTACG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.60% | 4.90% | 0.53% | 0.00% | NA |
| All Indica | 2759 | 98.80% | 1.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 85.80% | 12.60% | 1.59% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.60% | 0.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 96.80% | 3.20% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 98.60% | 0.10% | 1.30% | 0.00% | NA |
| Tropical Japonica | 504 | 61.50% | 36.10% | 2.38% | 0.00% | NA |
| Japonica Intermediate | 241 | 96.30% | 2.90% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 88.90% | 11.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0137140050 | A -> G | LOC_Os01g63970.1 | downstream_gene_variant ; 4658.0bp to feature; MODIFIER | silent_mutation | Average:42.432; most accessible tissue: Callus, score: 65.345 | N | N | N | N |
| vg0137140050 | A -> G | LOC_Os01g63970-LOC_Os01g63980 | intergenic_region ; MODIFIER | silent_mutation | Average:42.432; most accessible tissue: Callus, score: 65.345 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0137140050 | NA | 1.90E-06 | mr1633 | 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 |
| vg0137140050 | NA | 3.06E-06 | mr1870_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 |