| Variant ID: vg1109337009 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9337009 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CTCGCGAACCTTCCACAGACTAGGAGCTTAGAATTTCACCCAGGGTCCCCGGCCGAACCGGCAAAGGGGGACCTGCGCGGTCTCCCGGTGAGGAGCCTCA[A/C]
GCTCCGTCATCTGGCGCGCCAGGTAGGGGACTCTGCGTGTGATCTTCTAAGCTCTCGCACTCTTTCGTGTGCGTGAAGCTTTTCTTGTTCAGCCCAATGG
CCATTGGGCTGAACAAGAAAAGCTTCACGCACACGAAAGAGTGCGAGAGCTTAGAAGATCACACGCAGAGTCCCCTACCTGGCGCGCCAGATGACGGAGC[T/G]
TGAGGCTCCTCACCGGGAGACCGCGCAGGTCCCCCTTTGCCGGTTCGGCCGGGGACCCTGGGTGAAATTCTAAGCTCCTAGTCTGTGGAAGGTTCGCGAG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.20% | 0.10% | 12.42% | 32.23% | NA |
| All Indica | 2759 | 26.20% | 0.30% | 20.70% | 52.88% | NA |
| All Japonica | 1512 | 97.00% | 0.00% | 0.66% | 2.38% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.37% | 0.37% | NA |
| Indica I | 595 | 14.60% | 0.30% | 11.09% | 73.95% | NA |
| Indica II | 465 | 17.60% | 0.00% | 26.02% | 56.34% | NA |
| Indica III | 913 | 34.20% | 0.50% | 24.97% | 40.31% | NA |
| Indica Intermediate | 786 | 30.70% | 0.00% | 19.85% | 49.49% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.52% | 1.69% | NA |
| Tropical Japonica | 504 | 95.40% | 0.00% | 0.99% | 3.57% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.41% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 64.40% | 0.00% | 5.56% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109337009 | A -> DEL | N | N | silent_mutation | Average:11.839; most accessible tissue: Callus, score: 22.811 | N | N | N | N |
| vg1109337009 | A -> C | LOC_Os11g16810.1 | upstream_gene_variant ; 1715.0bp to feature; MODIFIER | silent_mutation | Average:11.839; most accessible tissue: Callus, score: 22.811 | N | N | N | N |
| vg1109337009 | A -> C | LOC_Os11g16820.1 | upstream_gene_variant ; 97.0bp to feature; MODIFIER | silent_mutation | Average:11.839; most accessible tissue: Callus, score: 22.811 | N | N | N | N |
| vg1109337009 | A -> C | LOC_Os11g16810-LOC_Os11g16820 | intergenic_region ; MODIFIER | silent_mutation | Average:11.839; most accessible tissue: Callus, score: 22.811 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1109337009 | NA | 2.50E-14 | mr1531 | 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 |
| vg1109337009 | 4.60E-06 | 4.60E-06 | mr1876 | 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 |
| vg1109337009 | NA | 9.71E-07 | mr1881 | 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 |
| vg1109337009 | NA | 3.43E-07 | mr1321_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 |
| vg1109337009 | NA | 4.28E-08 | mr1446_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 |
| vg1109337009 | NA | 2.23E-06 | mr1711_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 |
| vg1109337009 | NA | 5.04E-09 | mr1751_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 |
| vg1109337009 | NA | 1.12E-08 | mr1940_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 |