| Variant ID: vg1105816397 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5816397 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGTAGAAGAAACCTTTTGACAAAATATATATTTTCAAAGCATGGAGCAAATAGTCTGTTTCAATAATTCAGTGAATAATCTAAAAAGAACTAAGCCTAA[G/A]
CATAATTGTCATCTACTGGTATAACCAATTGACCATGTTGCAGGAAGAATGAACCCTGAAAATACATTCAGGCTGAAGATCAAACATTTTACAAATCGAG
CTCGATTTGTAAAATGTTTGATCTTCAGCCTGAATGTATTTTCAGGGTTCATTCTTCCTGCAACATGGTCAATTGGTTATACCAGTAGATGACAATTATG[C/T]
TTAGGCTTAGTTCTTTTTAGATTATTCACTGAATTATTGAAACAGACTATTTGCTCCATGCTTTGAAAATATATATTTTGTCAAAAGGTTTCTTCTACAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 62.10% | 4.10% | 3.85% | 29.92% | NA |
| All Indica | 2759 | 50.20% | 0.10% | 3.77% | 45.99% | NA |
| All Japonica | 1512 | 77.60% | 12.50% | 4.63% | 5.22% | NA |
| Aus | 269 | 95.50% | 1.10% | 0.74% | 2.60% | NA |
| Indica I | 595 | 79.20% | 0.00% | 3.19% | 17.65% | NA |
| Indica II | 465 | 18.10% | 0.00% | 8.82% | 73.12% | NA |
| Indica III | 913 | 45.80% | 0.00% | 1.20% | 53.01% | NA |
| Indica Intermediate | 786 | 52.30% | 0.30% | 4.20% | 43.26% | NA |
| Temperate Japonica | 767 | 63.10% | 22.00% | 8.60% | 6.26% | NA |
| Tropical Japonica | 504 | 95.80% | 0.40% | 0.20% | 3.57% | NA |
| Japonica Intermediate | 241 | 85.90% | 7.50% | 1.24% | 5.39% | NA |
| VI/Aromatic | 96 | 63.50% | 0.00% | 2.08% | 34.38% | NA |
| Intermediate | 90 | 65.60% | 1.10% | 4.44% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105816397 | G -> A | LOC_Os11g10600.1 | downstream_gene_variant ; 345.0bp to feature; MODIFIER | silent_mutation | Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1105816397 | G -> A | LOC_Os11g10610.1 | downstream_gene_variant ; 4436.0bp to feature; MODIFIER | silent_mutation | Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1105816397 | G -> A | LOC_Os11g10600-LOC_Os11g10610 | intergenic_region ; MODIFIER | silent_mutation | Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| vg1105816397 | G -> DEL | N | N | silent_mutation | Average:26.549; most accessible tissue: Zhenshan97 panicle, score: 65.386 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105816397 | 4.13E-06 | 5.64E-07 | mr1045 | 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 |
| vg1105816397 | NA | 9.64E-07 | mr1397 | 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 |
| vg1105816397 | NA | 6.86E-06 | mr1576 | 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 |