| Variant ID: vg0615635376 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 15635376 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAATAAATCAATTGGACGATGTCGAGAATCAGACTTATGTATGAATGGGCAAAGAACTCAGAATTCACATGACCAATTGGGCCAAAGTTCACAAGTCTGC[A/G]
TAGGAGAGCAACGGAGGAGGCCACCTGCCGATTTTGGGCCAGGCCGGCCCGACACATGGTTCGGCCGAACCCCCGCAGCGCCGTTCGATCCAGGTTTCTC
GAGAAACCTGGATCGAACGGCGCTGCGGGGGTTCGGCCGAACCATGTGTCGGGCCGGCCTGGCCCAAAATCGGCAGGTGGCCTCCTCCGTTGCTCTCCTA[T/C]
GCAGACTTGTGAACTTTGGCCCAATTGGTCATGTGAATTCTGAGTTCTTTGCCCATTCATACATAAGTCTGATTCTCGACATCGTCCAATTGATTTATTG
| 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 | 36.20% | 9.00% | 5.16% | 49.56% | NA |
| All Indica | 2759 | 3.50% | 11.70% | 5.65% | 79.09% | NA |
| All Japonica | 1512 | 91.30% | 1.00% | 1.46% | 6.22% | NA |
| Aus | 269 | 69.90% | 12.60% | 4.83% | 12.64% | NA |
| Indica I | 595 | 3.50% | 16.10% | 4.20% | 76.13% | NA |
| Indica II | 465 | 2.60% | 4.30% | 3.66% | 89.46% | NA |
| Indica III | 913 | 1.80% | 12.00% | 8.54% | 77.66% | NA |
| Indica Intermediate | 786 | 6.10% | 12.50% | 4.58% | 76.84% | NA |
| Temperate Japonica | 767 | 96.50% | 0.40% | 0.26% | 2.87% | NA |
| Tropical Japonica | 504 | 83.10% | 2.20% | 3.17% | 11.51% | NA |
| Japonica Intermediate | 241 | 92.10% | 0.40% | 1.66% | 5.81% | NA |
| VI/Aromatic | 96 | 5.20% | 46.90% | 46.88% | 1.04% | NA |
| Intermediate | 90 | 46.70% | 10.00% | 8.89% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0615635376 | A -> G | LOC_Os06g27630.1 | upstream_gene_variant ; 3557.0bp to feature; MODIFIER | silent_mutation | Average:13.254; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0615635376 | A -> G | LOC_Os06g27630-LOC_Os06g27640 | intergenic_region ; MODIFIER | silent_mutation | Average:13.254; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| vg0615635376 | A -> DEL | N | N | silent_mutation | Average:13.254; most accessible tissue: Zhenshan97 root, score: 23.888 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0615635376 | 1.25E-06 | NA | mr1253_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 |
| vg0615635376 | 1.03E-06 | NA | mr1253_2 | Ind_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 |