| Variant ID: vg1101529376 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 1529376 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 84. )
AAGTGCGGTCCTATCAATGCATAATATTTTTTAAGCAACATAATTATATTTCAAATATAGGCTCAAGATGTTCAAAGGTGGCTTGCCTTGCTCGAGATCT[A/G]
GAGCTTGATCCTCGAAATCCTCGCACTGCGGGTCTTCGGGCTCCGAAACTACACGCGAAACGGGACAACTCAACAAACGGCAAAAATAAAGCCCTATTAA
TTAATAGGGCTTTATTTTTGCCGTTTGTTGAGTTGTCCCGTTTCGCGTGTAGTTTCGGAGCCCGAAGACCCGCAGTGCGAGGATTTCGAGGATCAAGCTC[T/C]
AGATCTCGAGCAAGGCAAGCCACCTTTGAACATCTTGAGCCTATATTTGAAATATAATTATGTTGCTTAAAAAATATTATGCATTGATAGGACCGCACTT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.10% | 27.00% | 20.63% | 18.28% | NA |
| All Indica | 2759 | 2.30% | 41.70% | 27.44% | 28.60% | NA |
| All Japonica | 1512 | 96.20% | 0.10% | 1.19% | 2.45% | NA |
| Aus | 269 | 5.20% | 35.30% | 50.93% | 8.55% | NA |
| Indica I | 595 | 1.30% | 20.80% | 31.76% | 46.05% | NA |
| Indica II | 465 | 2.80% | 34.40% | 28.39% | 34.41% | NA |
| Indica III | 913 | 1.60% | 64.00% | 19.50% | 14.90% | NA |
| Indica Intermediate | 786 | 3.40% | 35.90% | 32.82% | 27.86% | NA |
| Temperate Japonica | 767 | 97.10% | 0.00% | 0.65% | 2.22% | NA |
| Tropical Japonica | 504 | 95.80% | 0.00% | 1.39% | 2.78% | NA |
| Japonica Intermediate | 241 | 94.20% | 0.80% | 2.49% | 2.49% | NA |
| VI/Aromatic | 96 | 36.50% | 13.50% | 50.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 16.70% | 16.67% | 16.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1101529376 | A -> DEL | N | N | silent_mutation | Average:16.966; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1101529376 | A -> G | LOC_Os11g03840.1 | upstream_gene_variant ; 4560.0bp to feature; MODIFIER | silent_mutation | Average:16.966; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1101529376 | A -> G | LOC_Os11g03840-LOC_Os11g03850 | intergenic_region ; MODIFIER | silent_mutation | Average:16.966; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1101529376 | 2.75E-06 | 2.75E-06 | mr1048 | 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 |
| vg1101529376 | NA | 6.52E-06 | mr1511 | 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 |
| vg1101529376 | 5.28E-06 | 5.26E-06 | mr1694 | 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 |
| vg1101529376 | 3.79E-07 | 3.79E-07 | mr1694 | 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 |
| vg1101529376 | NA | 9.07E-06 | mr1844 | 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 |