Variant ID: vg1206182541 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 6182541 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: Unkown |
Inferred Ancestral Allele: Not determined.
CTACATATAACTCTCCCCTAACCATCCACACCATGCTAAGGTTTCACCCCCACCCCCTACCCCGGAGGTGGGCAGTCCCCTCGTGCGCCGCGGTGAATCC[G/A]
GCAGCTGGACAACCGGACACCCCGGCCGACCCAACTCCATCACGCCCACCCTCACCACCGGTGCCTAGGAAAAGGTCGAGCTATACTTCAGATCAAGCAG
CTGCTTGATCTGAAGTATAGCTCGACCTTTTCCTAGGCACCGGTGGTGAGGGTGGGCGTGATGGAGTTGGGTCGGCCGGGGTGTCCGGTTGTCCAGCTGC[C/T]
GGATTCACCGCGGCGCACGAGGGGACTGCCCACCTCCGGGGTAGGGGGTGGGGGTGAAACCTTAGCATGGTGTGGATGGTTAGGGGAGAGTTATATGTAG
Populations | Population Size | Frequency of G(primary allele) | Frequency of Unkown(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 87.10% | 0.00% | 0.38% | 12.53% | NA |
All Indica | 2759 | 95.40% | 0.00% | 0.18% | 4.42% | NA |
All Japonica | 1512 | 71.10% | 0.00% | 0.60% | 28.31% | NA |
Aus | 269 | 89.20% | 0.00% | 1.49% | 9.29% | NA |
Indica I | 595 | 91.30% | 0.00% | 0.00% | 8.74% | NA |
Indica II | 465 | 96.60% | 0.00% | 0.22% | 3.23% | NA |
Indica III | 913 | 98.70% | 0.00% | 0.00% | 1.31% | NA |
Indica Intermediate | 786 | 94.00% | 0.00% | 0.51% | 5.47% | NA |
Temperate Japonica | 767 | 66.40% | 0.00% | 0.26% | 33.38% | NA |
Tropical Japonica | 504 | 79.40% | 0.00% | 1.19% | 19.44% | NA |
Japonica Intermediate | 241 | 68.90% | 0.00% | 0.41% | 30.71% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 81.10% | 0.00% | 0.00% | 18.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg1206182541 | G -> A | LOC_Os12g11430.1 | upstream_gene_variant ; 2819.0bp to feature; MODIFIER | N | Average:11.883; most accessible tissue: Callus, score: 31.81 | N | N | N | N |
vg1206182541 | G -> A | LOC_Os12g11440.1 | upstream_gene_variant ; 1482.0bp to feature; MODIFIER | N | Average:11.883; most accessible tissue: Callus, score: 31.81 | N | N | N | N |
vg1206182541 | G -> A | LOC_Os12g11430-LOC_Os12g11440 | intergenic_region ; MODIFIER | N | Average:11.883; most accessible tissue: Callus, score: 31.81 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1206182541 | 8.52E-07 | 8.52E-07 | mr1384 | 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 |