Variant ID: vg0523980909 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 23980909 |
Reference Allele: C | Alternative Allele: T |
Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.81, T: 0.19, others allele: 0.00, population size: 94. )
ATAAGATATAAATCACACTTAAAGTACTATGAGTGATAAAACATCTCATAGCAAAATAAATTATAATTACATAATTTTTTTTTTGAATAAGACGAATGGT[C/T]
AAACGTGTGAGAAAAAGTCAACGGCGTCATCTATTAAAAAACGGAGGGAGTACATATTTTGAATATGTAATTCGGTTTAGCTTTTCAGTGACATGTAAAA
TTTTACATGTCACTGAAAAGCTAAACCGAATTACATATTCAAAATATGTACTCCCTCCGTTTTTTAATAGATGACGCCGTTGACTTTTTCTCACACGTTT[G/A]
ACCATTCGTCTTATTCAAAAAAAAAATTATGTAATTATAATTTATTTTGCTATGAGATGTTTTATCACTCATAGTACTTTAAGTGTGATTTATATCTTAT
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 | 57.60% | 42.20% | 0.19% | 0.00% | NA |
All Indica | 2759 | 93.40% | 6.30% | 0.33% | 0.00% | NA |
All Japonica | 1512 | 0.60% | 99.40% | 0.00% | 0.00% | NA |
Aus | 269 | 30.90% | 69.10% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 93.50% | 6.00% | 0.43% | 0.00% | NA |
Indica III | 913 | 89.70% | 10.10% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 93.00% | 6.40% | 0.64% | 0.00% | NA |
Temperate Japonica | 767 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 1.80% | 98.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 0.00% | 100.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 2.10% | 97.90% | 0.00% | 0.00% | NA |
Intermediate | 90 | 57.80% | 42.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0523980909 | C -> T | LOC_Os05g40890.2 | downstream_gene_variant ; 1148.0bp to feature; MODIFIER | silent_mutation | Average:22.972; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
vg0523980909 | C -> T | LOC_Os05g40890-LOC_Os05g40900 | intergenic_region ; MODIFIER | silent_mutation | Average:22.972; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0523980909 | 1.46E-06 | 5.20E-06 | mr1084 | 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 |
vg0523980909 | NA | 2.28E-31 | mr1037_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 |