| Variant ID: vg0222134940 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22134940 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGAACATAATGGTGTGGAATAGGTGCGTTCGTTTCGAAAGATCTCTCGTTACTCATGCGGCGAACTTTTGTCATTTTGCTGATATTAGTACACGTGGGTG[C/A]
CATATTTTTTATCGGAACGAAAAGGTCAAAAAGCATCCAAACATGAGTTTTGGATATATTGGAGTGGATTGGGTGCGTCGGTTTCGAAAAACCTCCAATG
CATTGGAGGTTTTTCGAAACCGACGCACCCAATCCACTCCAATATATCCAAAACTCATGTTTGGATGCTTTTTGACCTTTTCGTTCCGATAAAAAATATG[G/T]
CACCCACGTGTACTAATATCAGCAAAATGACAAAAGTTCGCCGCATGAGTAACGAGAGATCTTTCGAAACGAACGCACCTATTCCACACCATTATGTTCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 93.60% | 0.10% | 1.14% | 5.14% | NA |
| All Indica | 2759 | 89.40% | 0.10% | 1.81% | 8.66% | 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 | 96.30% | 0.00% | 3.03% | 0.67% | NA |
| Indica II | 465 | 75.90% | 0.40% | 3.66% | 20.00% | NA |
| Indica III | 913 | 93.10% | 0.10% | 0.66% | 6.13% | NA |
| Indica Intermediate | 786 | 87.80% | 0.10% | 1.15% | 10.94% | 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 | 92.20% | 0.00% | 3.33% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222134940 | C -> A | LOC_Os02g36650.1 | upstream_gene_variant ; 3547.0bp to feature; MODIFIER | silent_mutation | Average:36.171; most accessible tissue: Callus, score: 78.763 | N | N | N | N |
| vg0222134940 | C -> A | LOC_Os02g36660.1 | upstream_gene_variant ; 1568.0bp to feature; MODIFIER | silent_mutation | Average:36.171; most accessible tissue: Callus, score: 78.763 | N | N | N | N |
| vg0222134940 | C -> A | LOC_Os02g36670.1 | downstream_gene_variant ; 576.0bp to feature; MODIFIER | silent_mutation | Average:36.171; most accessible tissue: Callus, score: 78.763 | N | N | N | N |
| vg0222134940 | C -> A | LOC_Os02g36660-LOC_Os02g36670 | intergenic_region ; MODIFIER | silent_mutation | Average:36.171; most accessible tissue: Callus, score: 78.763 | N | N | N | N |
| vg0222134940 | C -> DEL | N | N | silent_mutation | Average:36.171; most accessible tissue: Callus, score: 78.763 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222134940 | 3.58E-06 | 5.19E-06 | mr1146 | 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 |
| vg0222134940 | NA | 3.60E-06 | mr1833 | 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 |
| vg0222134940 | 4.00E-06 | 4.00E-06 | mr1847 | 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 |