| Variant ID: vg0401225967 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 1225967 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 259. )
CCAGAATTCTATATGAAAACGACAAGGACTACTCGGATTGTATCCATATTGGTTTCCCTAGTTCTACTTGGACAAGGGGACACCTATGGGTATAAATACA[A/T]
GGCCCCCCTAGGAGGAGAGGGGACACAATACACACCCACAATCAACATACATGGAACAACAGAAGCCAACATACGCCAAGACAAGACGCCGGATATCGAC
GTCGATATCCGGCGTCTTGTCTTGGCGTATGTTGGCTTCTGTTGTTCCATGTATGTTGATTGTGGGTGTGTATTGTGTCCCCTCTCCTCCTAGGGGGGCC[T/A]
TGTATTTATACCCATAGGTGTCCCCTTGTCCAAGTAGAACTAGGGAAACCAATATGGATACAATCCGAGTAGTCCTTGTCGTTTTCATATAGAATTCTGG
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 29.40% | 4.40% | 23.85% | 42.34% | NA |
| All Indica | 2759 | 23.20% | 7.50% | 23.99% | 45.34% | NA |
| All Japonica | 1512 | 38.20% | 0.10% | 14.95% | 46.69% | NA |
| Aus | 269 | 23.40% | 0.00% | 71.75% | 4.83% | NA |
| Indica I | 595 | 11.80% | 0.20% | 16.13% | 71.93% | NA |
| Indica II | 465 | 30.50% | 18.70% | 28.60% | 22.15% | NA |
| Indica III | 913 | 20.20% | 9.40% | 21.91% | 48.52% | NA |
| Indica Intermediate | 786 | 31.00% | 4.10% | 29.64% | 35.24% | NA |
| Temperate Japonica | 767 | 56.60% | 0.00% | 12.65% | 30.77% | NA |
| Tropical Japonica | 504 | 18.50% | 0.00% | 20.04% | 61.51% | NA |
| Japonica Intermediate | 241 | 21.20% | 0.80% | 11.62% | 66.39% | NA |
| VI/Aromatic | 96 | 78.10% | 0.00% | 14.58% | 7.29% | NA |
| Intermediate | 90 | 35.60% | 2.20% | 35.56% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0401225967 | A -> DEL | N | N | silent_mutation | Average:43.124; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0401225967 | A -> T | LOC_Os04g03000.1 | upstream_gene_variant ; 1616.0bp to feature; MODIFIER | silent_mutation | Average:43.124; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0401225967 | A -> T | LOC_Os04g03010.1 | upstream_gene_variant ; 526.0bp to feature; MODIFIER | silent_mutation | Average:43.124; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0401225967 | A -> T | LOC_Os04g02990.1 | downstream_gene_variant ; 4538.0bp to feature; MODIFIER | silent_mutation | Average:43.124; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0401225967 | A -> T | LOC_Os04g03020.1 | downstream_gene_variant ; 3935.0bp to feature; MODIFIER | silent_mutation | Average:43.124; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| vg0401225967 | A -> T | LOC_Os04g03000-LOC_Os04g03010 | intergenic_region ; MODIFIER | silent_mutation | Average:43.124; most accessible tissue: Minghui63 panicle, score: 73.225 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0401225967 | 9.43E-06 | NA | mr1094_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 |
| vg0401225967 | 2.12E-06 | NA | mr1096_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 |
| vg0401225967 | 7.90E-07 | NA | mr1121_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 |