Variant ID: vg0432418113 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 32418113 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.08, others allele: 0.00, population size: 309. )
GCTGTGTCAGCACTGACCAGTGTTGTTAACGATGACATTAAACCACTCAACAGGTCTAGTGGCTCTGAACTGAAGACTCAATGGCAACCAGATTCTAAGA[C/T]
TGATGCTTCCGTTCTGAAGATCTCTAAAGTCGAGACAAGCCTGCAGTTTGATGACAAAGCTAGGGATGGTTATGATGGAGATGAACATGAATGCACAGCC
GGCTGTGCATTCATGTTCATCTCCATCATAACCATCCCTAGCTTTGTCATCAAACTGCAGGCTTGTCTCGACTTTAGAGATCTTCAGAACGGAAGCATCA[G/A]
TCTTAGAATCTGGTTGCCATTGAGTCTTCAGTTCAGAGCCACTAGACCTGTTGAGTGGTTTAATGTCATCGTTAACAACACTGGTCAGTGCTGACACAGC
Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 59.60% | 40.20% | 0.04% | 0.21% | NA |
All Indica | 2759 | 75.60% | 24.10% | 0.00% | 0.29% | NA |
All Japonica | 1512 | 25.60% | 74.20% | 0.07% | 0.13% | NA |
Aus | 269 | 80.70% | 19.30% | 0.00% | 0.00% | NA |
Indica I | 595 | 83.70% | 15.80% | 0.00% | 0.50% | NA |
Indica II | 465 | 59.60% | 40.00% | 0.00% | 0.43% | NA |
Indica III | 913 | 85.90% | 14.00% | 0.00% | 0.11% | NA |
Indica Intermediate | 786 | 67.20% | 32.60% | 0.00% | 0.25% | NA |
Temperate Japonica | 767 | 23.30% | 76.70% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 30.40% | 69.00% | 0.20% | 0.40% | NA |
Japonica Intermediate | 241 | 22.80% | 77.20% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 78.10% | 21.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 54.40% | 44.40% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0432418113 | C -> DEL | N | N | silent_mutation | Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |
vg0432418113 | C -> T | LOC_Os04g54500.1 | upstream_gene_variant ; 250.0bp to feature; MODIFIER | silent_mutation | Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |
vg0432418113 | C -> T | LOC_Os04g54490.1 | downstream_gene_variant ; 2500.0bp to feature; MODIFIER | silent_mutation | Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |
vg0432418113 | C -> T | LOC_Os04g54490-LOC_Os04g54500 | intergenic_region ; MODIFIER | silent_mutation | Average:51.028; most accessible tissue: Zhenshan97 young leaf, score: 66.83 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0432418113 | 5.84E-07 | 6.62E-12 | mr1741_2 | 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 |
vg0432418113 | NA | 1.71E-09 | mr1785_2 | 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 |
vg0432418113 | 2.09E-06 | NA | mr1800_2 | 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 |