| Variant ID: vg0905620924 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5620924 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 236. )
GAGGCACTAATCCTGCCTTGCGTCGGAGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCAACGATCTAACGAGGCACTAATCCCGCCTTGCGTCG[A/G]
AGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCTCTCTTTCTTCTGGATCTTCCTCCTCTGGGGTAGCTGACGGCGGTGCTTCTCCCTTGAGCTC
GAGCTCAAGGGAGAAGCACCGCCGTCAGCTACCCCAGAGGAGGAAGATCCAGAAGAAAGAGAGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCT[T/C]
CGACGCAAGGCGGGATTAGTGCCTCGTTAGATCGTTGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCTCCGACGCAAGGCAGGATTAGTGCCTC
| 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 | 65.70% | 28.60% | 0.53% | 5.23% | NA |
| All Indica | 2759 | 91.40% | 3.10% | 0.76% | 4.68% | NA |
| All Japonica | 1512 | 19.90% | 80.00% | 0.07% | 0.07% | NA |
| Aus | 269 | 49.80% | 7.40% | 0.37% | 42.38% | NA |
| Indica I | 595 | 89.70% | 3.50% | 0.34% | 6.39% | NA |
| Indica II | 465 | 97.00% | 2.60% | 0.22% | 0.22% | NA |
| Indica III | 913 | 92.90% | 2.30% | 1.42% | 3.40% | NA |
| Indica Intermediate | 786 | 87.80% | 4.10% | 0.64% | 7.51% | NA |
| Temperate Japonica | 767 | 10.00% | 89.80% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 18.80% | 81.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 53.50% | 46.10% | 0.00% | 0.41% | NA |
| VI/Aromatic | 96 | 92.70% | 4.20% | 1.04% | 2.08% | NA |
| Intermediate | 90 | 62.20% | 35.60% | 1.11% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0905620924 | A -> G | LOC_Os09g10310.1 | missense_variant ; p.Phe202Ser; MODERATE | nonsynonymous_codon ; F202S | Average:49.692; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | unknown | unknown | TOLERATED | 1.00 |
| vg0905620924 | A -> DEL | LOC_Os09g10310.1 | N | frameshift_variant | Average:49.692; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0905620924 | NA | 2.96E-12 | mr1034 | 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 |
| vg0905620924 | NA | 4.29E-22 | mr1163 | 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 |
| vg0905620924 | NA | 9.62E-08 | mr1700_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 |