Variant ID: vg0902040540 (JBrowse) | Variation Type: SNP |
Chromosome: chr09 | Position: 2040540 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 286. )
CTGAAGACGAAGTTAGAAGACTAAGGCTCAAACCCCAGTTGAGTTTTGCCTGTGGAGTGGAGTTGAAGCCCAGCTAGGATCGCCTTTTCCGCTGCTGCTG[C/T]
TTTCGTTTCGGTGTGAGGACTAAGTGCCTCTTCTGTAAGTATTTTACGCTTTATTTATGTTTGGATCTGTATATTAAGAGGCGGCATTCCAGATGCTGAA
TTCAGCATCTGGAATGCCGCCTCTTAATATACAGATCCAAACATAAATAAAGCGTAAAATACTTACAGAAGAGGCACTTAGTCCTCACACCGAAACGAAA[G/A]
CAGCAGCAGCGGAAAAGGCGATCCTAGCTGGGCTTCAACTCCACTCCACAGGCAAAACTCAACTGGGGTTTGAGCCTTAGTCTTCTAACTTCGTCTTCAG
Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 92.60% | 7.40% | 0.00% | 0.00% | NA |
All Indica | 2759 | 95.40% | 4.60% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 19.00% | 81.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 93.30% | 6.70% | 0.00% | 0.00% | NA |
Indica III | 913 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 92.40% | 7.60% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0902040540 | C -> T | LOC_Os09g03960.1 | upstream_gene_variant ; 3133.0bp to feature; MODIFIER | silent_mutation | Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
vg0902040540 | C -> T | LOC_Os09g03970.1 | upstream_gene_variant ; 245.0bp to feature; MODIFIER | silent_mutation | Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
vg0902040540 | C -> T | LOC_Os09g03980.1 | upstream_gene_variant ; 3161.0bp to feature; MODIFIER | silent_mutation | Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
vg0902040540 | C -> T | LOC_Os09g03960-LOC_Os09g03970 | intergenic_region ; MODIFIER | silent_mutation | Average:56.763; most accessible tissue: Zhenshan97 panicle, score: 77.482 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0902040540 | NA | 1.00E-07 | mr1193 | 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 |
vg0902040540 | NA | 4.71E-12 | mr1471 | 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 |
vg0902040540 | NA | 1.00E-11 | mr1722 | 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 |
vg0902040540 | 9.70E-06 | 4.17E-09 | mr1808 | 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 |
vg0902040540 | NA | 1.79E-20 | mr1855 | 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 |
vg0902040540 | NA | 5.01E-21 | mr1855_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 |