Variant ID: vg0123011670 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 23011670 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AGATCCTCCATTAATATTGATCTTGCATACCAGGATAACATGCCAAGTGCACGTGACATTTCTCAGCAATCTTCAATAGCATATAAAAAAGATGGGATCG[C/T]
CATCGCTCGACTCGAACTCACATAAAAACCAATCTTTTTCCTAGACCTACTCTACTAGAAAAACCATTTTTTCCCGACGATGTCATTTTTTTTCCAGGCG
CGCCTGGAAAAAAAATGACATCGTCGGGAAAAAATGGTTTTTCTAGTAGAGTAGGTCTAGGAAAAAGATTGGTTTTTATGTGAGTTCGAGTCGAGCGATG[G/A]
CGATCCCATCTTTTTTATATGCTATTGAAGATTGCTGAGAAATGTCACGTGCACTTGGCATGTTATCCTGGTATGCAAGATCAATATTAATGGAGGATCT
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 | 84.50% | 15.50% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 53.50% | 46.50% | 0.00% | 0.00% | NA |
Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 17.60% | 82.40% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 78.40% | 21.60% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 80.00% | 20.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0123011670 | C -> T | LOC_Os01g40720.1 | upstream_gene_variant ; 2729.0bp to feature; MODIFIER | silent_mutation | Average:59.168; most accessible tissue: Minghui63 root, score: 73.73 | N | N | N | N |
vg0123011670 | C -> T | LOC_Os01g40730.1 | downstream_gene_variant ; 1754.0bp to feature; MODIFIER | silent_mutation | Average:59.168; most accessible tissue: Minghui63 root, score: 73.73 | N | N | N | N |
vg0123011670 | C -> T | LOC_Os01g40740.1 | downstream_gene_variant ; 3837.0bp to feature; MODIFIER | silent_mutation | Average:59.168; most accessible tissue: Minghui63 root, score: 73.73 | N | N | N | N |
vg0123011670 | C -> T | LOC_Os01g40720-LOC_Os01g40730 | intergenic_region ; MODIFIER | silent_mutation | Average:59.168; most accessible tissue: Minghui63 root, score: 73.73 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0123011670 | NA | 9.68E-10 | mr1712 | 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 |
vg0123011670 | NA | 9.55E-07 | mr1977 | 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 |
vg0123011670 | NA | 3.68E-08 | mr1378_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 |
vg0123011670 | 2.59E-06 | 1.23E-07 | mr1826_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 |