| Variant ID: vg1105316445 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5316445 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 182. )
TCTAGAGTCTCGTCTTTCGTTTTCAACAAGTACACATAGCAAAATATAGTAGCATCATCAATCAACGTCATGAAATATCGTTTTCCACCCTTCATCAACA[C/A]
CCCCATTCATTTCACAAAGATCTGAATGTAGGAGTTCTAGTGGTGCCAAGTTTCTCTCCTCGGCAGCCTTGTGAGGCTTGCGAGGTTGCTTCGATTGTAC
GTACAATCGAAGCAACCTCGCAAGCCTCACAAGGCTGCCGAGGAGAGAAACTTGGCACCACTAGAACTCCTACATTCAGATCTTTGTGAAATGAATGGGG[G/T]
TGTTGATGAAGGGTGGAAAACGATATTTCATGACGTTGATTGATGATGCTACTATATTTTGCTATGTGTACTTGTTGAAAACGAAAGACGAGACTCTAGA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 40.80% | 0.10% | 2.69% | 56.41% | NA |
| All Indica | 2759 | 40.30% | 0.00% | 1.81% | 57.88% | NA |
| All Japonica | 1512 | 48.10% | 0.30% | 0.66% | 50.93% | NA |
| Aus | 269 | 8.20% | 1.10% | 21.56% | 69.14% | NA |
| Indica I | 595 | 36.30% | 0.00% | 1.34% | 62.35% | NA |
| Indica II | 465 | 21.10% | 0.00% | 0.43% | 78.49% | NA |
| Indica III | 913 | 48.60% | 0.00% | 2.96% | 48.41% | NA |
| Indica Intermediate | 786 | 45.00% | 0.00% | 1.65% | 53.31% | NA |
| Temperate Japonica | 767 | 76.00% | 0.30% | 0.26% | 23.47% | NA |
| Tropical Japonica | 504 | 14.90% | 0.20% | 1.39% | 83.53% | NA |
| Japonica Intermediate | 241 | 29.00% | 0.40% | 0.41% | 70.12% | NA |
| VI/Aromatic | 96 | 24.00% | 0.00% | 5.21% | 70.83% | NA |
| Intermediate | 90 | 45.60% | 0.00% | 4.44% | 50.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105316445 | C -> A | LOC_Os11g09919.1 | missense_variant ; p.Val3Leu; MODERATE | nonsynonymous_codon ; V3L | Average:5.716; most accessible tissue: Callus, score: 12.051 | unknown | unknown | DELETERIOUS | 0.01 |
| vg1105316445 | C -> DEL | LOC_Os11g09919.1 | N | frameshift_variant | Average:5.716; most accessible tissue: Callus, score: 12.051 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1105316445 | 8.01E-06 | 8.01E-06 | mr1141_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 |
| vg1105316445 | NA | 1.47E-06 | mr1829_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 |
| vg1105316445 | 3.24E-06 | 2.56E-08 | mr1842_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 |