| Variant ID: vg1108224521 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8224521 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 69. )
TATATTGTCCCTAATTTTTAATGTTGTTGAACACAAAATAGGATTGCATTGAAGCTATTGATGGCACACATATTAGAGCCTCTGTTCGTAAGAATGTTGA[A/G]
TCTTCATTCCGTGGTAGGAAGTCCCATGCCACTCAAATTTTAATGGTGGCCGTAGATTTTGATCTTCGGTTTACTTTTGTCCTGGCTAGTTGGGAGGGGA
TCCCCTCCCAACTAGCCAGGACAAAAGTAAACCGAAGATCAAAATCTACGGCCACCATTAAAATTTGAGTGGCATGGGACTTCCTACCACGGAATGAAGA[T/C]
TCAACATTCTTACGAACAGAGGCTCTAATATGTGTGCCATCAATAGCTTCAATGCAATCCTATTTTGTGTTCAACAACATTAAAAATTAGGGACAATATA
| 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 | 56.20% | 24.20% | 1.40% | 18.22% | NA |
| All Indica | 2759 | 67.50% | 3.30% | 1.05% | 28.16% | NA |
| All Japonica | 1512 | 28.60% | 65.10% | 1.85% | 4.43% | NA |
| Aus | 269 | 94.80% | 1.90% | 1.86% | 1.49% | NA |
| Indica I | 595 | 78.50% | 6.70% | 1.34% | 13.45% | NA |
| Indica II | 465 | 44.30% | 1.10% | 0.86% | 53.76% | NA |
| Indica III | 913 | 74.80% | 0.80% | 0.66% | 23.77% | NA |
| Indica Intermediate | 786 | 64.40% | 5.00% | 1.40% | 29.26% | NA |
| Temperate Japonica | 767 | 10.60% | 88.10% | 1.17% | 0.13% | NA |
| Tropical Japonica | 504 | 57.10% | 32.90% | 2.38% | 7.54% | NA |
| Japonica Intermediate | 241 | 26.60% | 58.90% | 2.90% | 11.62% | NA |
| VI/Aromatic | 96 | 54.20% | 42.70% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 61.10% | 23.30% | 3.33% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108224521 | A -> DEL | LOC_Os11g14600.1 | N | frameshift_variant | Average:16.184; most accessible tissue: Callus, score: 43.972 | N | N | N | N |
| vg1108224521 | A -> G | LOC_Os11g14600.1 | synonymous_variant ; p.Glu74Glu; LOW | synonymous_codon | Average:16.184; most accessible tissue: Callus, score: 43.972 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108224521 | NA | 4.32E-07 | mr1584 | 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 |
| vg1108224521 | NA | 9.27E-06 | mr1657 | 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 |
| vg1108224521 | 3.35E-06 | NA | mr1717 | 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 |
| vg1108224521 | NA | 3.68E-06 | mr1860 | 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 |
| vg1108224521 | NA | 4.34E-08 | mr1401_2 | 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 |