Variant ID: vg0621807445 (JBrowse) | Variation Type: SNP |
Chromosome: chr06 | Position: 21807445 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.51, A: 0.49, others allele: 0.00, population size: 94. )
CCTTGGGATTCTTACCACCCTATTGGTTTGAGACATTCTTTGTCAAGTTTGACATATATCCTTATGTATTAGGGACATCTATATGCAAAAAGTTTGAGTG[G/A]
TTTGGTAGGCAACGACAAAATCAACATGATAAATGTATTTTGGATGTCAAATCGTGCCCATGGAGAATGTGGCACATTTTGACAAATATGCTTGTAAAAG
CTTTTACAAGCATATTTGTCAAAATGTGCCACATTCTCCATGGGCACGATTTGACATCCAAAATACATTTATCATGTTGATTTTGTCGTTGCCTACCAAA[C/T]
CACTCAAACTTTTTGCATATAGATGTCCCTAATACATAAGGATATATGTCAAACTTGACAAAGAATGTCTCAAACCAATAGGGTGGTAAGAATCCCAAGG
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 | 75.70% | 24.30% | 0.04% | 0.00% | NA |
All Indica | 2759 | 81.00% | 19.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 79.40% | 20.50% | 0.13% | 0.00% | NA |
Aus | 269 | 3.00% | 97.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
Indica II | 465 | 80.00% | 20.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 70.90% | 29.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 81.80% | 18.20% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 79.90% | 19.90% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 77.40% | 22.40% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 81.70% | 18.30% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 67.70% | 32.30% | 0.00% | 0.00% | NA |
Intermediate | 90 | 75.60% | 24.40% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0621807445 | G -> A | LOC_Os06g36990.1 | upstream_gene_variant ; 1983.0bp to feature; MODIFIER | silent_mutation | Average:51.282; most accessible tissue: Callus, score: 83.27 | N | N | N | N |
vg0621807445 | G -> A | LOC_Os06g36980-LOC_Os06g36990 | intergenic_region ; MODIFIER | silent_mutation | Average:51.282; most accessible tissue: Callus, score: 83.27 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0621807445 | NA | 7.80E-06 | mr1382 | 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 |
vg0621807445 | 3.02E-06 | NA | mr1398 | 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 |
vg0621807445 | NA | 1.75E-07 | mr1057_2 | 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 |
vg0621807445 | NA | 1.15E-08 | mr1126_2 | 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 |
vg0621807445 | NA | 7.20E-06 | mr1827_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 |