Variant ID: vg0503966024 (JBrowse) | Variation Type: SNP |
Chromosome: chr05 | Position: 3966024 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 277. )
ATGTCTTACTACTACATAATTCATTTTTACAGAAATCTTCCTTTATTTTTACAAATCATAAAAGATGACCCTTATGTGAATGTACGAGATATACCATCAA[G/A]
GACTGCATATGAAAATTGATTTCCACAGGCGGGCCTATTAAGTTTAGCTATGTACACGCACACCTTGCTCTCTCGTGCGTACCACTATGTCCCCTCCCTC
GAGGGAGGGGACATAGTGGTACGCACGAGAGAGCAAGGTGTGCGTGTACATAGCTAAACTTAATAGGCCCGCCTGTGGAAATCAATTTTCATATGCAGTC[C/T]
TTGATGGTATATCTCGTACATTCACATAAGGGTCATCTTTTATGATTTGTAAAAATAAAGGAAGATTTCTGTAAAAATGAATTATGTAGTAGTAAGACAT
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 | 87.00% | 9.80% | 1.76% | 1.48% | NA |
All Indica | 2759 | 82.60% | 15.50% | 1.85% | 0.04% | NA |
All Japonica | 1512 | 93.60% | 0.10% | 1.79% | 4.56% | NA |
Aus | 269 | 91.80% | 8.20% | 0.00% | 0.00% | NA |
Indica I | 595 | 83.00% | 12.90% | 4.03% | 0.00% | NA |
Indica II | 465 | 88.40% | 10.50% | 1.08% | 0.00% | NA |
Indica III | 913 | 74.40% | 24.80% | 0.88% | 0.00% | NA |
Indica Intermediate | 786 | 88.40% | 9.70% | 1.78% | 0.13% | NA |
Temperate Japonica | 767 | 97.70% | 0.00% | 2.22% | 0.13% | NA |
Tropical Japonica | 504 | 96.80% | 0.20% | 0.20% | 2.78% | NA |
Japonica Intermediate | 241 | 73.90% | 0.00% | 3.73% | 22.41% | NA |
VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
Intermediate | 90 | 90.00% | 4.40% | 5.56% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0503966024 | G -> DEL | N | N | silent_mutation | Average:57.45; most accessible tissue: Zhenshan97 young leaf, score: 82.539 | N | N | N | N |
vg0503966024 | G -> A | LOC_Os05g07440.1 | downstream_gene_variant ; 1215.0bp to feature; MODIFIER | silent_mutation | Average:57.45; most accessible tissue: Zhenshan97 young leaf, score: 82.539 | N | N | N | N |
vg0503966024 | G -> A | LOC_Os05g07450.1 | downstream_gene_variant ; 4946.0bp to feature; MODIFIER | silent_mutation | Average:57.45; most accessible tissue: Zhenshan97 young leaf, score: 82.539 | N | N | N | N |
vg0503966024 | G -> A | LOC_Os05g07430-LOC_Os05g07440 | intergenic_region ; MODIFIER | silent_mutation | Average:57.45; most accessible tissue: Zhenshan97 young leaf, score: 82.539 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0503966024 | 5.13E-06 | NA | mr1005 | 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 |
vg0503966024 | 2.02E-07 | NA | mr1005 | 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 |
vg0503966024 | NA | 8.37E-07 | mr1498_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 |
vg0503966024 | NA | 6.49E-07 | mr1925_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 |