Variant ID: vg0527788086 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 27788086 |
Reference Allele: T | Alternative Allele: G |
Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 120. )
TATGGTAGTACTCGAGTTGTGAAGTTACTGATGAAAACATTCAAACTGAATTTGGTTGCTGCATTTAGGATGTCATAGGTATTTTCTTTTTTAATCTCTC[T/G]
CGCTGATTTGGTTTCATTTCATTTAGATGAGTATTGAAAACCTTTCTCTTGTGACAATTTTATTCAGTTATGTATTTCATTCAGCTGATGAATTATCCTT
AAGGATAATTCATCAGCTGAATGAAATACATAACTGAATAAAATTGTCACAAGAGAAAGGTTTTCAATACTCATCTAAATGAAATGAAACCAAATCAGCG[A/C]
GAGAGATTAAAAAAGAAAATACCTATGACATCCTAAATGCAGCAACCAAATTCAGTTTGAATGTTTTCATCAGTAACTTCACAACTCGAGTACTACCATA
Populations | Population Size | Frequency of T(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 99.70% | 0.20% | 0.06% | 0.00% | NA |
All Indica | 2759 | 99.50% | 0.40% | 0.11% | 0.00% | NA |
All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 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 | 98.90% | 0.90% | 0.22% | 0.00% | NA |
Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 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 | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0527788086 | T -> G | LOC_Os05g48450.1 | downstream_gene_variant ; 3254.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48480.1 | downstream_gene_variant ; 2116.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48489.1 | downstream_gene_variant ; 4285.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48450.2 | downstream_gene_variant ; 3254.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48450.4 | downstream_gene_variant ; 3254.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48450.5 | downstream_gene_variant ; 3254.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48450.6 | downstream_gene_variant ; 3254.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48450.3 | downstream_gene_variant ; 3254.0bp to feature; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
vg0527788086 | T -> G | LOC_Os05g48470.1 | intron_variant ; MODIFIER | N | Average:13.803; most accessible tissue: Minghui63 flower, score: 19.775 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0527788086 | 5.77E-06 | NA | mr1016 | 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 |
vg0527788086 | 2.63E-06 | 9.81E-11 | mr1016 | 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 |
vg0527788086 | NA | 5.19E-10 | mr1018 | Jap_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 |
vg0527788086 | NA | 4.77E-09 | mr1019 | Jap_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 |
vg0527788086 | NA | 3.01E-11 | mr1055 | Jap_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 |
vg0527788086 | NA | 9.06E-06 | mr1557 | Jap_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 |
vg0527788086 | NA | 1.62E-10 | mr1720 | 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 |
vg0527788086 | NA | 1.24E-06 | mr1780 | Jap_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 |
vg0527788086 | NA | 6.78E-06 | mr1817 | Jap_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 |
vg0527788086 | NA | 5.02E-12 | mr1938 | 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 |
vg0527788086 | NA | 1.31E-10 | mr1019_2 | Jap_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 |
vg0527788086 | 5.80E-07 | 8.12E-12 | mr1055_2 | Jap_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 |