Variant ID: vg0118123199 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 18123199 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCTCAGTTCAGACTATCCGATCACATAGAACTATCCGACCTGATATCAGACAATCCGACCCTGTTTTGTTTTAGCTTCCGCATTTATTTTAAAAATCAC[C/A]
TATTCACCCCCCTCTAGGCGACATCAAGGTCCTTTCAGTTATAATAGTTAACATTTAATTAATCGTGTGCTACTGAGCTTTATCGTTTCGGTTTTTAAAA
TTTTAAAAACCGAAACGATAAAGCTCAGTAGCACACGATTAATTAAATGTTAACTATTATAACTGAAAGGACCTTGATGTCGCCTAGAGGGGGGTGAATA[G/T]
GTGATTTTTAAAATAAATGCGGAAGCTAAAACAAAACAGGGTCGGATTGTCTGATATCAGGTCGGATAGTTCTATGTGATCGGATAGTCTGAACTGAGAT
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 | 98.60% | 1.40% | 0.06% | 0.00% | NA |
All Indica | 2759 | 97.60% | 2.30% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 89.50% | 10.10% | 0.43% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.00% | 0.11% | 0.00% | NA |
Indica Intermediate | 786 | 98.30% | 1.70% | 0.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0118123199 | C -> A | LOC_Os01g33000.1 | upstream_gene_variant ; 1730.0bp to feature; MODIFIER | silent_mutation | Average:65.78; most accessible tissue: Callus, score: 81.157 | N | N | N | N |
vg0118123199 | C -> A | LOC_Os01g32990.1 | downstream_gene_variant ; 2050.0bp to feature; MODIFIER | silent_mutation | Average:65.78; most accessible tissue: Callus, score: 81.157 | N | N | N | N |
vg0118123199 | C -> A | LOC_Os01g32990-LOC_Os01g33000 | intergenic_region ; MODIFIER | silent_mutation | Average:65.78; most accessible tissue: Callus, score: 81.157 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0118123199 | NA | 2.09E-08 | mr1711_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 |