| Variant ID: vg1108343418 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 8343418 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 74. )
ACCGCCGTTGCCCGAGCGATCCGTCTACGCAGCCGCCGGGGGGACGACCGCGTCGAGGGCCAAGGCCGGTGTCACTGGATTCCCTCCGCCGCGTTGCTCC[C/T]
GATGACGCCCCCGATTCTACCGGTCTAGGCCGCCGGCCACCGGGTCCCCTAGGATGGCGCCCCCGACTCCACCACGCCATTTCGATGTGGGCCTGCTCCA
TGGAGCAGGCCCACATCGAAATGGCGTGGTGGAGTCGGGGGCGCCATCCTAGGGGACCCGGTGGCCGGCGGCCTAGACCGGTAGAATCGGGGGCGTCATC[G/A]
GGAGCAACGCGGCGGAGGGAATCCAGTGACACCGGCCTTGGCCCTCGACGCGGTCGTCCCCCCGGCGGCTGCGTAGACGGATCGCTCGGGCAACGGCGGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 61.20% | 36.80% | 1.61% | 0.38% | NA |
| All Indica | 2759 | 53.80% | 44.80% | 1.16% | 0.22% | NA |
| All Japonica | 1512 | 72.10% | 24.70% | 2.51% | 0.73% | NA |
| Aus | 269 | 75.50% | 23.40% | 0.74% | 0.37% | NA |
| Indica I | 595 | 30.10% | 66.60% | 3.36% | 0.00% | NA |
| Indica II | 465 | 83.70% | 15.50% | 0.86% | 0.00% | NA |
| Indica III | 913 | 51.60% | 48.30% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 56.60% | 41.70% | 0.89% | 0.76% | NA |
| Temperate Japonica | 767 | 88.80% | 8.20% | 3.00% | 0.00% | NA |
| Tropical Japonica | 504 | 46.20% | 50.20% | 1.39% | 2.18% | NA |
| Japonica Intermediate | 241 | 73.00% | 23.70% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 63.50% | 36.50% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 61.10% | 34.40% | 4.44% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1108343418 | C -> T | LOC_Os11g14820.1 | synonymous_variant ; p.Ser34Ser; LOW | synonymous_codon | Average:44.54; most accessible tissue: Zhenshan97 young leaf, score: 71.065 | N | N | N | N |
| vg1108343418 | C -> DEL | LOC_Os11g14820.1 | N | frameshift_variant | Average:44.54; most accessible tissue: Zhenshan97 young leaf, score: 71.065 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1108343418 | NA | 8.24E-06 | mr1188 | 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 |
| vg1108343418 | 2.03E-06 | 2.03E-06 | mr1717 | 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 |