Variant ID: vg0220005783 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 20005783 |
Reference Allele: G | Alternative Allele: T |
Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCATAAGGATTTAAATTTCTTTGTTTTACCTAGCTCACAGAAAAACTCATAAGAATTTAAATTTCTCTAAAATTCCTTTAATTTTTTTTTCAATCCAAAA[G/T]
ATTTTCCTTACATTTCGCAAGTCGAAGAACAAATTTGAAACCAAAACATGTAAGGAGAACAAAATAAAAAAAAAATCTTAGAACTTGGAAGCGTAAAAGG
CCTTTTACGCTTCCAAGTTCTAAGATTTTTTTTTTATTTTGTTCTCCTTACATGTTTTGGTTTCAAATTTGTTCTTCGACTTGCGAAATGTAAGGAAAAT[C/A]
TTTTGGATTGAAAAAAAAATTAAAGGAATTTTAGAGAAATTTAAATTCTTATGAGTTTTTCTGTGAGCTAGGTAAAACAAAGAAATTTAAATCCTTATGA
Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 97.30% | 1.90% | 0.78% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 91.50% | 6.00% | 2.45% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 86.30% | 9.10% | 4.56% | 0.00% | NA |
Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 90.50% | 8.70% | 0.83% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 100.00% | 0.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0220005783 | G -> T | LOC_Os02g33610.1 | upstream_gene_variant ; 180.0bp to feature; MODIFIER | silent_mutation | Average:91.82; most accessible tissue: Callus, score: 95.084 | N | N | N | N |
vg0220005783 | G -> T | LOC_Os02g33610.2 | upstream_gene_variant ; 170.0bp to feature; MODIFIER | silent_mutation | Average:91.82; most accessible tissue: Callus, score: 95.084 | N | N | N | N |
vg0220005783 | G -> T | LOC_Os02g33600.1 | downstream_gene_variant ; 3962.0bp to feature; MODIFIER | silent_mutation | Average:91.82; most accessible tissue: Callus, score: 95.084 | N | N | N | N |
vg0220005783 | G -> T | LOC_Os02g33600-LOC_Os02g33610 | intergenic_region ; MODIFIER | silent_mutation | Average:91.82; most accessible tissue: Callus, score: 95.084 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0220005783 | NA | 5.61E-06 | mr1416_2 | Jap_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 |