Variant ID: vg0133452014 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 33452014 |
Reference Allele: C | Alternative Allele: A |
Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCTGATCCTAATGAATCTAGGTTTTCACCCGGAGAAATCTCTTGAAGTTGAGTTGAATGAGGGCTCCAGTAGCAACACCTTCGAGAAGGTGAACGGCGCC[C/A]
AAAGGGGTTACCGTTGCTAGCACCGAGAGCGGAGCAAGGCTTTTGCCTTGGAGCACCCATCAACCATAGCATCCAAGGCGGGAGCCACCAAATGTTACCT
AGGTAACATTTGGTGGCTCCCGCCTTGGATGCTATGGTTGATGGGTGCTCCAAGGCAAAAGCCTTGCTCCGCTCTCGGTGCTAGCAACGGTAACCCCTTT[G/T]
GGCGCCGTTCACCTTCTCGAAGGTGTTGCTACTGGAGCCCTCATTCAACTCAACTTCAAGAGATTTCTCCGGGTGAAAACCTAGATTCATTAGGATCAGA
Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
All Indica | 2759 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 35.70% | 64.30% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.20% | 2.80% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 97.80% | 2.20% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0133452014 | C -> A | LOC_Os01g57854.1 | upstream_gene_variant ; 1419.0bp to feature; MODIFIER | silent_mutation | Average:68.951; most accessible tissue: Zhenshan97 flower, score: 80.904 | N | N | N | N |
vg0133452014 | C -> A | LOC_Os01g57840.1 | downstream_gene_variant ; 2666.0bp to feature; MODIFIER | silent_mutation | Average:68.951; most accessible tissue: Zhenshan97 flower, score: 80.904 | N | N | N | N |
vg0133452014 | C -> A | LOC_Os01g57840-LOC_Os01g57854 | intergenic_region ; MODIFIER | silent_mutation | Average:68.951; most accessible tissue: Zhenshan97 flower, score: 80.904 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0133452014 | NA | 1.18E-06 | mr1320 | 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 |
vg0133452014 | 4.95E-06 | NA | mr1379_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 |
vg0133452014 | NA | 4.87E-08 | mr1510_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 |