| Variant ID: vg0224728169 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 24728169 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 263. )
GATTTTGTAATTAGTTTTTTTTCATAAATACCCGAAAACCTCATGTGACACCTATATAATATCCGACGTGACACGCCAAAATTTTACACCACTAGATCTA[A/G]
ACACCCCCTTTTGTTGAAGTCTGGAGCCTCAAGGAAAAGAGCTTACCAGGCTTCTAGACGTGCAAAAGAAGATTTATAAAACAAAAGGTATTTATTACAA
TTGTAATAAATACCTTTTGTTTTATAAATCTTCTTTTGCACGTCTAGAAGCCTGGTAAGCTCTTTTCCTTGAGGCTCCAGACTTCAACAAAAGGGGGTGT[T/C]
TAGATCTAGTGGTGTAAAATTTTGGCGTGTCACGTCGGATATTATATAGGTGTCACATGAGGTTTTCGGGTATTTATGAAAAAAAACTAATTACAAAATC
| 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 | 76.00% | 6.70% | 10.07% | 7.24% | NA |
| All Indica | 2759 | 72.70% | 8.60% | 12.69% | 6.05% | NA |
| All Japonica | 1512 | 86.20% | 4.50% | 0.66% | 8.66% | NA |
| Aus | 269 | 57.20% | 0.40% | 31.97% | 10.41% | NA |
| Indica I | 595 | 82.70% | 13.90% | 3.03% | 0.34% | NA |
| Indica II | 465 | 58.90% | 1.70% | 29.25% | 10.11% | NA |
| Indica III | 913 | 79.10% | 4.90% | 8.32% | 7.67% | NA |
| Indica Intermediate | 786 | 65.90% | 12.70% | 15.27% | 6.11% | NA |
| Temperate Japonica | 767 | 94.70% | 5.20% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 69.20% | 5.00% | 0.99% | 24.80% | NA |
| Japonica Intermediate | 241 | 94.60% | 1.20% | 1.66% | 2.49% | NA |
| VI/Aromatic | 96 | 61.50% | 5.20% | 22.92% | 10.42% | NA |
| Intermediate | 90 | 76.70% | 7.80% | 8.89% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0224728169 | A -> G | LOC_Os02g40784.1 | upstream_gene_variant ; 4049.0bp to feature; MODIFIER | silent_mutation | Average:66.148; most accessible tissue: Minghui63 panicle, score: 88.595 | N | N | N | N |
| vg0224728169 | A -> G | LOC_Os02g40784.3 | upstream_gene_variant ; 4065.0bp to feature; MODIFIER | silent_mutation | Average:66.148; most accessible tissue: Minghui63 panicle, score: 88.595 | N | N | N | N |
| vg0224728169 | A -> G | LOC_Os02g40800.1 | downstream_gene_variant ; 2667.0bp to feature; MODIFIER | silent_mutation | Average:66.148; most accessible tissue: Minghui63 panicle, score: 88.595 | N | N | N | N |
| vg0224728169 | A -> G | LOC_Os02g40810.1 | downstream_gene_variant ; 76.0bp to feature; MODIFIER | silent_mutation | Average:66.148; most accessible tissue: Minghui63 panicle, score: 88.595 | N | N | N | N |
| vg0224728169 | A -> G | LOC_Os02g40800-LOC_Os02g40810 | intergenic_region ; MODIFIER | silent_mutation | Average:66.148; most accessible tissue: Minghui63 panicle, score: 88.595 | N | N | N | N |
| vg0224728169 | A -> DEL | N | N | silent_mutation | Average:66.148; most accessible tissue: Minghui63 panicle, score: 88.595 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0224728169 | 1.05E-06 | 1.05E-06 | mr1664 | 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 |
| vg0224728169 | 4.28E-07 | 4.28E-07 | mr1848 | 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 |
| vg0224728169 | NA | 5.93E-06 | mr1533_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 |