Variant ID: vg0809823253 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 9823253 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CTGTGAAAACCAAGCCAAGCTTAAGCCAACCATTCTTGATCTCGAGCGGATAAGGCCGGGAGGAGGGCTCGGTCTCTCCCTGGTCTCCAATTTCTCTCGC[G/A]
CTCCCCTCTCTCTCCCCCGCGCGCGCTCATCTCTCTCTCATCCCAACGGCGGCGGCCGGATCTTGCTGTGGCCCGACAGCAGCGGTACCACCCTCCCCTC
GAGGGGAGGGTGGTACCGCTGCTGTCGGGCCACAGCAAGATCCGGCCGCCGCCGTTGGGATGAGAGAGAGATGAGCGCGCGCGGGGGAGAGAGAGGGGAG[C/T]
GCGAGAGAAATTGGAGACCAGGGAGAGACCGAGCCCTCCTCCCGGCCTTATCCGCTCGAGATCAAGAATGGTTGGCTTAAGCTTGGCTTGGTTTTCACAG
Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 93.50% | 6.20% | 0.25% | 0.00% | NA |
All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 86.80% | 12.40% | 0.73% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 96.20% | 2.30% | 1.43% | 0.00% | NA |
Tropical Japonica | 504 | 70.40% | 29.60% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 91.30% | 8.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
Intermediate | 90 | 83.30% | 15.60% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0809823253 | G -> A | LOC_Os08g16100.1 | upstream_gene_variant ; 4851.0bp to feature; MODIFIER | silent_mutation | Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
vg0809823253 | G -> A | LOC_Os08g16110.1 | upstream_gene_variant ; 1633.0bp to feature; MODIFIER | silent_mutation | Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
vg0809823253 | G -> A | LOC_Os08g16120.1 | upstream_gene_variant ; 1374.0bp to feature; MODIFIER | silent_mutation | Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
vg0809823253 | G -> A | LOC_Os08g16120.2 | upstream_gene_variant ; 1374.0bp to feature; MODIFIER | silent_mutation | Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
vg0809823253 | G -> A | LOC_Os08g16110-LOC_Os08g16120 | intergenic_region ; MODIFIER | silent_mutation | Average:66.37; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0809823253 | 1.99E-08 | NA | Heading_date | All | YES | Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652 |
vg0809823253 | NA | 3.32E-09 | mr1570 | 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 |