Variant ID: vg0131651142 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 31651142 |
Reference Allele: G | Alternative Allele: T |
Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 117. )
GTTTTATGGTTCAAGTTGTAGAAAACCACACACATTTTAACACTTGGCACTTAAGTATATATATTTTGGTAGTTTAGTTTCACAAAACCACACTATCCAT[G/T]
AATGGATTTACCCGCGAGATGACGTGGTTGTTCCATCTAGGATGGGGACGTGGCATCCTGTTAATTTTGTCTGATGGCTGGTAATATGATGCCATGTCCT
AGGACATGGCATCATATTACCAGCCATCAGACAAAATTAACAGGATGCCACGTCCCCATCCTAGATGGAACAACCACGTCATCTCGCGGGTAAATCCATT[C/A]
ATGGATAGTGTGGTTTTGTGAAACTAAACTACCAAAATATATATACTTAAGTGCCAAGTGTTAAAATGTGTGTGGTTTTCTACAACTTGAACCATAAAAC
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 | 88.70% | 10.60% | 0.70% | 0.00% | NA |
All Indica | 2759 | 80.60% | 18.20% | 1.20% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 96.10% | 3.00% | 0.84% | 0.00% | NA |
Indica II | 465 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
Indica III | 913 | 62.80% | 36.70% | 0.55% | 0.00% | NA |
Indica Intermediate | 786 | 80.30% | 16.80% | 2.93% | 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 | 98.90% | 1.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0131651142 | G -> T | LOC_Os01g55040.1 | upstream_gene_variant ; 2386.0bp to feature; MODIFIER | silent_mutation | Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 | N | N | N | N |
vg0131651142 | G -> T | LOC_Os01g55050.1 | downstream_gene_variant ; 474.0bp to feature; MODIFIER | silent_mutation | Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 | N | N | N | N |
vg0131651142 | G -> T | LOC_Os01g55050.2 | downstream_gene_variant ; 474.0bp to feature; MODIFIER | silent_mutation | Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 | N | N | N | N |
vg0131651142 | G -> T | LOC_Os01g55040-LOC_Os01g55050 | intergenic_region ; MODIFIER | silent_mutation | Average:79.97; most accessible tissue: Zhenshan97 root, score: 91.517 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0131651142 | 5.00E-06 | NA | mr1973 | 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 |
vg0131651142 | 2.03E-06 | 1.19E-06 | mr1973 | Ind_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 |
vg0131651142 | 6.97E-06 | NA | mr1970_2 | Ind_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 |
vg0131651142 | 6.75E-08 | NA | mr1973_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 |
vg0131651142 | 2.97E-09 | 7.78E-08 | mr1973_2 | Ind_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 |