| Variant ID: vg1116571839 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 16571839 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTATTATCGATGAGAGTGGATTTACAATCTACAGGCGAAGAAATGATGGAAGAACTATCATTAAAAATGGGATCCCTTTGGATAATAGATCGGTTGTACC[G/A]
TACAATATGAAACTGCTTAAAACATATGAGGCACACATAAACGTTGAATGGTTTGAAAAACGTCGCAAAACGATCAATGCTTACCGAATGGTTTGAAACT
AGTTTCAAACCATTCGGTAAGCATTGATCGTTTTGCGACGTTTTTCAAACCATTCAACGTTTATGTGTGCCTCATATGTTTTAAGCAGTTTCATATTGTA[C/T]
GGTACAACCGATCTATTATCCAAAGGGATCCCATTTTTAATGATAGTTCTTCCATCATTTCTTCGCCTGTAGATTGTAAATCCACTCTCATCGATAATAG
| 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 | 85.70% | 2.00% | 0.85% | 11.49% | NA |
| All Indica | 2759 | 78.30% | 3.30% | 1.23% | 17.18% | NA |
| All Japonica | 1512 | 95.80% | 0.10% | 0.40% | 3.70% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 88.40% | 8.90% | 0.34% | 2.35% | NA |
| Indica II | 465 | 73.80% | 0.00% | 1.51% | 24.73% | NA |
| Indica III | 913 | 73.80% | 1.10% | 1.31% | 23.77% | NA |
| Indica Intermediate | 786 | 78.40% | 3.70% | 1.65% | 16.28% | NA |
| Temperate Japonica | 767 | 97.80% | 0.00% | 0.52% | 1.69% | NA |
| Tropical Japonica | 504 | 92.10% | 0.00% | 0.40% | 7.54% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.40% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 1.10% | 0.00% | 14.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1116571839 | G -> A | LOC_Os11g28650.1 | synonymous_variant ; p.Pro484Pro; LOW | synonymous_codon | Average:37.083; most accessible tissue: Zhenshan97 young leaf, score: 53.969 | N | N | N | N |
| vg1116571839 | G -> DEL | LOC_Os11g28650.1 | N | frameshift_variant | Average:37.083; most accessible tissue: Zhenshan97 young leaf, score: 53.969 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1116571839 | NA | 9.21E-06 | mr1008_2 | Ind_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 |
| vg1116571839 | 3.20E-07 | 2.44E-09 | mr1959_2 | Ind_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 |