Variant ID: vg1202415264 (JBrowse) | Variation Type: SNP |
Chromosome: chr12 | Position: 2415264 |
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: 313. )
GGACAAGGGGACACCTATAGGTATAAATACAAGCCCCCCTAGGAGGAGAGGGAGGAGGATCAACACCCAACACAATCGACATAGAAGCCACAACATAGAA[G/A]
TCTACATACGCCAAGACATGCCGCCGGATATCGACTTCAGGGATAAGCACGGCTAGTACCCTACGGTGTCTCCGGATACTGTCAGGAGAGACAAAAGCGC
GCGCTTTTGTCTCTCCTGACAGTATCCGGAGACACCGTAGGGTACTAGCCGTGCTTATCCCTGAAGTCGATATCCGGCGGCATGTCTTGGCGTATGTAGA[C/T]
TTCTATGTTGTGGCTTCTATGTCGATTGTGTTGGGTGTTGATCCTCCTCCCTCTCCTCCTAGGGGGGCTTGTATTTATACCTATAGGTGTCCCCTTGTCC
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 | 98.30% | 1.30% | 0.36% | 0.00% | NA |
All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 94.80% | 4.10% | 1.12% | 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 | 94.00% | 4.30% | 1.69% | 0.00% | NA |
Tropical Japonica | 504 | 99.40% | 0.40% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 87.60% | 11.20% | 1.24% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg1202415264 | G -> A | LOC_Os12g05360.1 | upstream_gene_variant ; 2692.0bp to feature; MODIFIER | silent_mutation | Average:48.332; most accessible tissue: Minghui63 root, score: 58.187 | N | N | N | N |
vg1202415264 | G -> A | LOC_Os12g05350.1 | downstream_gene_variant ; 3146.0bp to feature; MODIFIER | silent_mutation | Average:48.332; most accessible tissue: Minghui63 root, score: 58.187 | N | N | N | N |
vg1202415264 | G -> A | LOC_Os12g05350-LOC_Os12g05360 | intergenic_region ; MODIFIER | silent_mutation | Average:48.332; most accessible tissue: Minghui63 root, score: 58.187 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg1202415264 | 4.26E-10 | NA | mr1549 | 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 |
vg1202415264 | 5.37E-06 | NA | mr1550 | 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 |
vg1202415264 | 2.28E-08 | NA | mr1757 | 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 |