Variant ID: vg0825346100 (JBrowse) | Variation Type: SNP |
Chromosome: chr08 | Position: 25346100 |
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, A: 0.01, others allele: 0.00, population size: 295. )
ATGCAAATGATGCCTATTCAACCCAGTGTCACCATGTGGGGAAGCATGATGAATGGTTGCAAGGTACATGGCAGGGCTGATATTGCTGAGAGGGTAGGAA[G/A]
GCAGGTTGCTGAGCTTAATCCTCAGTTTGGCGCAATATATGTGATAATGTCCAATATATATGCGGAGATTGGTAGGTGGCATGCAGTGGAGCACACCAGG
CCTGGTGTGCTCCACTGCATGCCACCTACCAATCTCCGCATATATATTGGACATTATCACATATATTGCGCCAAACTGAGGATTAAGCTCAGCAACCTGC[C/T]
TTCCTACCCTCTCAGCAATATCAGCCCTGCCATGTACCTTGCAACCATTCATCATGCTTCCCCACATGGTGACACTGGGTTGAATAGGCATCATTTGCAT
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 | 94.90% | 5.10% | 0.00% | 0.00% | NA |
All Indica | 2759 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Aus | 269 | 33.80% | 66.20% | 0.00% | 0.00% | NA |
Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica III | 913 | 96.20% | 3.80% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 97.30% | 2.70% | 0.00% | 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 | 96.90% | 3.10% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0825346100 | G -> A | LOC_Os08g40020.1 | missense_variant ; p.Arg455Lys; MODERATE | nonsynonymous_codon ; R455K | Average:62.299; most accessible tissue: Callus, score: 69.474 | unknown | unknown | TOLERATED | 0.43 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0825346100 | NA | 7.36E-06 | mr1349 | 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 |
vg0825346100 | NA | 7.03E-12 | mr1918_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 |