| Variant ID: vg1106872087 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 6872087 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTAGCATATCACATAAAAGACTGACTCCATGTTTCTGTTCTTCAGCACTGATGGCGGAGGCAGTAATCCTTGCCATCTCAAAGATTGGTACCACTTTAGG[A/G]
GAAGAAGCCACCAAGGCTGTTCTAGCAAAACTGTCTGAAAAGGTAACAAATTTGAAAAATCTGCCAAGGAATGTAACAAGAATAGAAAAGGAACTGAAGA
TCTTCAGTTCCTTTTCTATTCTTGTTACATTCCTTGGCAGATTTTTCAAATTTGTTACCTTTTCAGACAGTTTTGCTAGAACAGCCTTGGTGGCTTCTTC[T/C]
CCTAAAGTGGTACCAATCTTTGAGATGGCAAGGATTACTGCCTCCGCCATCAGTGCTGAAGAACAGAAACATGGAGTCAGTCTTTTATGTGATATGCTAA
| 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 | 41.30% | 24.20% | 0.51% | 33.94% | NA |
| All Indica | 2759 | 47.60% | 2.30% | 0.58% | 49.51% | NA |
| All Japonica | 1512 | 20.80% | 65.40% | 0.53% | 13.23% | NA |
| Aus | 269 | 97.00% | 0.40% | 0.00% | 2.60% | NA |
| Indica I | 595 | 26.20% | 2.00% | 1.01% | 70.76% | NA |
| Indica II | 465 | 28.00% | 0.90% | 0.65% | 70.54% | NA |
| Indica III | 913 | 69.70% | 3.20% | 0.11% | 27.05% | NA |
| Indica Intermediate | 786 | 49.70% | 2.40% | 0.76% | 47.07% | NA |
| Temperate Japonica | 767 | 22.00% | 73.50% | 0.39% | 4.04% | NA |
| Tropical Japonica | 504 | 21.20% | 54.00% | 0.60% | 24.21% | NA |
| Japonica Intermediate | 241 | 16.20% | 63.50% | 0.83% | 19.50% | NA |
| VI/Aromatic | 96 | 22.90% | 75.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 45.60% | 22.20% | 0.00% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1106872087 | A -> DEL | LOC_Os11g12300.1 | N | frameshift_variant | Average:19.033; most accessible tissue: Minghui63 root, score: 31.271 | N | N | N | N |
| vg1106872087 | A -> G | LOC_Os11g12300.1 | synonymous_variant ; p.Gly17Gly; LOW | synonymous_codon | Average:19.033; most accessible tissue: Minghui63 root, score: 31.271 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1106872087 | 5.26E-07 | NA | mr1567_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 |
| vg1106872087 | 7.10E-07 | 4.88E-07 | mr1567_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 |
| vg1106872087 | NA | 5.67E-06 | mr1693_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 |
| vg1106872087 | NA | 3.68E-09 | mr1947_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 |