Variant ID: vg1125096005 (JBrowse) | Variation Type: SNP |
Chromosome: chr11 | Position: 25096005 |
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: 236. )
ATTTCAAGTAGTATATATATACTTCTTTCGTCCCAAAATAGACTAATCTCATGCGAAATGTGACACATCGTAGTACTACGAATCTAGAACTGAAACGGGG[T/G]
TTGGAACTATTCCGGCTCACATAATATAATGGAGCAGCCGCTCATGCTTACATGCTCACTAGCAATGTATACTCCTACATTGTAGCATGTAATTAAGTAC
GTACTTAATTACATGCTACAATGTAGGAGTATACATTGCTAGTGAGCATGTAAGCATGAGCGGCTGCTCCATTATATTATGTGAGCCGGAATAGTTCCAA[A/C]
CCCCGTTTCAGTTCTAGATTCGTAGTACTACGATGTGTCACATTTCGCATGAGATTAGTCTATTTTGGGACGAAAGAAGTATATATATACTACTTGAAAT
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 | 99.00% | 1.00% | 0.02% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 97.10% | 2.80% | 0.07% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 94.90% | 5.00% | 0.13% | 0.00% | NA |
Tropical Japonica | 504 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 98.30% | 1.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 96.70% | 3.30% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1125096005 | T -> G | LOC_Os11g41770.1 | downstream_gene_variant ; 4782.0bp to feature; MODIFIER | silent_mutation | Average:41.03; most accessible tissue: Zhenshan97 young leaf, score: 69.263 | N | N | N | N |
vg1125096005 | T -> G | LOC_Os11g41760-LOC_Os11g41770 | intergenic_region ; MODIFIER | silent_mutation | Average:41.03; most accessible tissue: Zhenshan97 young leaf, score: 69.263 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1125096005 | NA | 5.26E-06 | mr1100_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 |
vg1125096005 | NA | 3.26E-06 | mr1402_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 |
vg1125096005 | NA | 2.35E-06 | mr1613_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 |
vg1125096005 | 1.61E-08 | 1.89E-10 | mr1795_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 |
vg1125096005 | NA | 6.96E-06 | mr1913_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 |
vg1125096005 | NA | 6.99E-07 | mr1962_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 |