| Variant ID: vg0315390589 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 15390589 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TCAAACTTCCAACTTTGCCATCACATCAAAATTTTCCTACACATACAAACTTCCAACTTTTCCGTCGTATCGTCCCAATTTCAACCAAACTTTCAATTTT[A/G]
ACGTGAACTAAACACACCATTCGGGCCTAGCGAGGCATATAGCTCCTGCATCATATCATGCGTTTGTATATGCTACGTACGTGAGTGCTTGCTCGATCGT
ACGATCGAGCAAGCACTCACGTACGTAGCATATACAAACGCATGATATGATGCAGGAGCTATATGCCTCGCTAGGCCCGAATGGTGTGTTTAGTTCACGT[T/C]
AAAATTGAAAGTTTGGTTGAAATTGGGACGATACGACGGAAAAGTTGGAAGTTTGTATGTGTAGGAAAATTTTGATGTGATGGCAAAGTTGGAAGTTTGA
| 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 | 88.20% | 11.80% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 91.80% | 8.20% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 81.50% | 18.50% | 0.00% | 0.00% | NA |
| Aus | 269 | 87.70% | 12.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.40% | 6.60% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 85.80% | 14.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 93.30% | 6.60% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 61.30% | 38.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 75.10% | 24.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 91.70% | 8.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 86.70% | 13.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0315390589 | A -> G | LOC_Os03g26920.1 | upstream_gene_variant ; 4738.0bp to feature; MODIFIER | silent_mutation | Average:54.58; most accessible tissue: Zhenshan97 flower, score: 84.504 | N | N | N | N |
| vg0315390589 | A -> G | LOC_Os03g26910-LOC_Os03g26920 | intergenic_region ; MODIFIER | silent_mutation | Average:54.58; most accessible tissue: Zhenshan97 flower, score: 84.504 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0315390589 | 1.84E-06 | NA | mr1176 | 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 |
| vg0315390589 | NA | 3.39E-07 | mr1623_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 |