| Variant ID: vg0220569457 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20569457 |
| Reference Allele: A | Alternative Allele: C |
| Primary Allele: A | Secondary Allele: C |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 128. )
ATTAACTTAATGAGTTTATAACTAAAAATCTAAGTACACACATATCACAGTCCTTAGTTTGTCCATGAGGTATAATAAGAGAGCTGGGTGTGATGGAATC[A/C]
ATCGAATGATAGATTTAACCAGTGCAATATCCTATATAGTAGTATATATATAATTTGGTTGACGCCTATTATTTAACAGAACAATAAATAACTCATGTTC
GAACATGAGTTATTTATTGTTCTGTTAAATAATAGGCGTCAACCAAATTATATATATACTACTATATAGGATATTGCACTGGTTAAATCTATCATTCGAT[T/G]
GATTCCATCACACCCAGCTCTCTTATTATACCTCATGGACAAACTAAGGACTGTGATATGTGTGTACTTAGATTTTTAGTTATAAACTCATTAAGTTAAT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 94.40% | 2.80% | 1.97% | 0.83% | NA |
| All Indica | 2759 | 90.60% | 4.70% | 3.23% | 1.41% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.60% | 1.50% | 0.50% | 0.34% | NA |
| Indica II | 465 | 81.10% | 11.80% | 5.81% | 1.29% | NA |
| Indica III | 913 | 94.00% | 1.40% | 2.63% | 1.97% | NA |
| Indica Intermediate | 786 | 87.00% | 6.90% | 4.45% | 1.65% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.00% | 0.41% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0220569457 | A -> DEL | N | N | silent_mutation | Average:61.999; most accessible tissue: Minghui63 panicle, score: 85.069 | N | N | N | N |
| vg0220569457 | A -> C | LOC_Os02g34380.1 | upstream_gene_variant ; 2813.0bp to feature; MODIFIER | silent_mutation | Average:61.999; most accessible tissue: Minghui63 panicle, score: 85.069 | N | N | N | N |
| vg0220569457 | A -> C | LOC_Os02g34370.1 | downstream_gene_variant ; 3793.0bp to feature; MODIFIER | silent_mutation | Average:61.999; most accessible tissue: Minghui63 panicle, score: 85.069 | N | N | N | N |
| vg0220569457 | A -> C | LOC_Os02g34370-LOC_Os02g34380 | intergenic_region ; MODIFIER | silent_mutation | Average:61.999; most accessible tissue: Minghui63 panicle, score: 85.069 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0220569457 | NA | 9.44E-06 | mr1750 | 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 |
| vg0220569457 | 1.22E-06 | 7.14E-08 | mr1877 | 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 |
| vg0220569457 | NA | 3.32E-06 | mr1929 | 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 |