Variant ID: vg0200926863 (JBrowse) | Variation Type: SNP |
Chromosome: chr02 | Position: 926863 |
Reference Allele: A | Alternative Allele: G |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 300. )
GAAGTGAAGCTGTACTCTGAATTAAGATTGTGTAAACACAGCATATAAAAGGTTGCATACAGATATGCAGTATTTCAAAAATACATGAAAAATAGTCCAA[A/G]
TATTTTCTGTAAGAACTATAACTACAAGAAAGACTATAATTTTAAGCAACTTTGGCAAAAGTACCTTCAATGTGATGCTAGAGCCAAACCAAACATCACC
GGTGATGTTTGGTTTGGCTCTAGCATCACATTGAAGGTACTTTTGCCAAAGTTGCTTAAAATTATAGTCTTTCTTGTAGTTATAGTTCTTACAGAAAATA[T/C]
TTGGACTATTTTTCATGTATTTTTGAAATACTGCATATCTGTATGCAACCTTTTATATGCTGTGTTTACACAATCTTAATTCAGAGTACAGCTTCACTTC
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 95.90% | 2.20% | 1.84% | 0.00% | NA |
All Indica | 2759 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
All Japonica | 1512 | 88.00% | 6.90% | 5.16% | 0.00% | NA |
Aus | 269 | 99.60% | 0.00% | 0.37% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.10% | 0.00% | 0.86% | 0.00% | NA |
Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.70% | 0.00% | 0.25% | 0.00% | NA |
Temperate Japonica | 767 | 83.10% | 9.00% | 7.95% | 0.00% | NA |
Tropical Japonica | 504 | 98.80% | 0.20% | 0.99% | 0.00% | NA |
Japonica Intermediate | 241 | 80.90% | 14.10% | 4.98% | 0.00% | NA |
VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Intermediate | 90 | 96.70% | 1.10% | 2.22% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0200926863 | A -> G | LOC_Os02g02540.1 | downstream_gene_variant ; 2893.0bp to feature; MODIFIER | silent_mutation | Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 | N | N | N | N |
vg0200926863 | A -> G | LOC_Os02g02550.1 | downstream_gene_variant ; 231.0bp to feature; MODIFIER | silent_mutation | Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 | N | N | N | N |
vg0200926863 | A -> G | LOC_Os02g02570.1 | downstream_gene_variant ; 3389.0bp to feature; MODIFIER | silent_mutation | Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 | N | N | N | N |
vg0200926863 | A -> G | LOC_Os02g02560.1 | intron_variant ; MODIFIER | silent_mutation | Average:43.622; most accessible tissue: Minghui63 flower, score: 56.131 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0200926863 | NA | 6.19E-06 | mr1201 | 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 |
vg0200926863 | 1.03E-06 | 2.87E-07 | mr1274 | 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 |