| Variant ID: vg1125837262 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 25837262 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, A: 0.08, others allele: 0.00, population size: 105. )
TTGGGATTATTTCATTTCTTTTTAAATATGGCATGTAGCTTGGTTGAATACACGTGCCGAGCAACATAAGACAATTCCTGAATTAAAAACATTGACGCTT[G/A]
TATCAACTGTTAGCGCCCGTATAGAGCTTACGTTGTGGAATAAAAATAAGGGTAATTTTCATCAAACTCCGTAAAGGTGCAGGTTATAAAAAATCACAGA
TCTGTGATTTTTTATAACCTGCACCTTTACGGAGTTTGATGAAAATTACCCTTATTTTTATTCCACAACGTAAGCTCTATACGGGCGCTAACAGTTGATA[C/T]
AAGCGTCAATGTTTTTAATTCAGGAATTGTCTTATGTTGCTCGGCACGTGTATTCAACCAAGCTACATGCCATATTTAAAAAGAAATGAAATAATCCCAA
| 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 | 81.00% | 13.00% | 5.97% | 0.00% | NA |
| All Indica | 2759 | 75.00% | 15.70% | 9.39% | 0.00% | NA |
| All Japonica | 1512 | 95.40% | 3.80% | 0.79% | 0.00% | NA |
| Aus | 269 | 56.50% | 42.00% | 1.49% | 0.00% | NA |
| Indica I | 595 | 87.70% | 8.90% | 3.36% | 0.00% | NA |
| Indica II | 465 | 90.80% | 3.40% | 5.81% | 0.00% | NA |
| Indica III | 913 | 60.60% | 24.60% | 14.79% | 0.00% | NA |
| Indica Intermediate | 786 | 72.60% | 17.60% | 9.80% | 0.00% | NA |
| Temperate Japonica | 767 | 98.00% | 2.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 92.50% | 5.60% | 1.98% | 0.00% | NA |
| Japonica Intermediate | 241 | 93.40% | 5.80% | 0.83% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 12.20% | 7.78% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1125837262 | G -> A | LOC_Os11g42890.1 | upstream_gene_variant ; 564.0bp to feature; MODIFIER | silent_mutation | Average:34.798; most accessible tissue: Callus, score: 68.761 | N | N | N | N |
| vg1125837262 | G -> A | LOC_Os11g42880.1 | downstream_gene_variant ; 3837.0bp to feature; MODIFIER | silent_mutation | Average:34.798; most accessible tissue: Callus, score: 68.761 | N | N | N | N |
| vg1125837262 | G -> A | LOC_Os11g42900.1 | downstream_gene_variant ; 3331.0bp to feature; MODIFIER | silent_mutation | Average:34.798; most accessible tissue: Callus, score: 68.761 | N | N | N | N |
| vg1125837262 | G -> A | LOC_Os11g42890-LOC_Os11g42900 | intergenic_region ; MODIFIER | silent_mutation | Average:34.798; most accessible tissue: Callus, score: 68.761 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1125837262 | 7.89E-10 | 7.89E-10 | mr1191 | 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 |
| vg1125837262 | 3.22E-14 | 3.22E-14 | mr1644 | 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 |
| vg1125837262 | 1.28E-13 | 1.28E-13 | mr1191_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 |