| Variant ID: vg0220506753 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20506753 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 82. )
GTGTGCTGGGCCTTCGCCGCCCATGTAATAAATTAACTATTTACGCTTCCGCTTGATAAACTCTGAAATGTATCAACTTTTGGTGTACCTTACCTCCTGG[A/G]
ACAAGGAATAATACACGCACGTAAGGAACGCCTGTTGGGTTAATTCCGGTCGTGACAAATTTTGACATTATAAATTTTTAGCTTGTCAATAAAGTTAAGC
GCTTAACTTTATTGACAAGCTAAAAATTTATAATGTCAAAATTTGTCACGACCGGAATTAACCCAACAGGCGTTCCTTACGTGCGTGTATTATTCCTTGT[T/C]
CCAGGAGGTAAGGTACACCAAAAGTTGATACATTTCAGAGTTTATCAAGCGGAAGCGTAAATAGTTAATTTATTACATGGGCGGCGAAGGCCCAGCACAC
| 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 | 27.40% | 9.80% | 1.67% | 61.07% | NA |
| All Indica | 2759 | 4.10% | 1.80% | 0.72% | 93.29% | NA |
| All Japonica | 1512 | 67.90% | 26.90% | 3.57% | 1.65% | NA |
| Aus | 269 | 5.20% | 0.40% | 0.00% | 94.42% | NA |
| Indica I | 595 | 1.20% | 1.80% | 1.85% | 95.13% | NA |
| Indica II | 465 | 8.80% | 2.20% | 0.22% | 88.82% | NA |
| Indica III | 913 | 3.40% | 0.40% | 0.33% | 95.84% | NA |
| Indica Intermediate | 786 | 4.50% | 3.30% | 0.64% | 91.60% | NA |
| Temperate Japonica | 767 | 41.70% | 50.70% | 6.52% | 1.04% | NA |
| Tropical Japonica | 504 | 96.60% | 1.20% | 0.79% | 1.39% | NA |
| Japonica Intermediate | 241 | 91.30% | 4.60% | 0.00% | 4.15% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 55.60% | 6.70% | 5.56% | 32.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0220506753 | A -> G | LOC_Os02g34280.1 | upstream_gene_variant ; 1801.0bp to feature; MODIFIER | silent_mutation | Average:29.087; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg0220506753 | A -> G | LOC_Os02g34270-LOC_Os02g34280 | intergenic_region ; MODIFIER | silent_mutation | Average:29.087; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg0220506753 | A -> DEL | N | N | silent_mutation | Average:29.087; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220506753 | NA | 4.85E-14 | Spikelet_length | All | Not | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
| vg0220506753 | NA | 1.17E-06 | mr1271 | 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 |
| vg0220506753 | NA | 3.45E-07 | mr1271 | 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 |
| vg0220506753 | 4.08E-06 | NA | mr1765 | 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 |
| vg0220506753 | NA | 1.46E-08 | mr1543_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 |
| vg0220506753 | NA | 8.83E-06 | mr1588_2 | 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 |
| vg0220506753 | NA | 2.37E-07 | mr1748_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 |
| vg0220506753 | NA | 1.20E-06 | mr1768_2 | 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 |