Variant ID: vg0107544024 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 7544024 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 259. )
TGATAAATACATCAAAACTTTTTATTGATAGTGAAATTATTGACTGCAAGTTTTTGCCAATAGTGAAATCATCGAAAGTGAAACCATTAGAAGCATTTAT[G/A]
AAATCATCGATAGGGAAAGGTTTGACAATAGTGAAATCATTTACGGTAAGTTTTTACCAAAGAACTTACATAAATGCTATAAGGGAAGAAAAAATGTGGT
ACCACATTTTTTCTTCCCTTATAGCATTTATGTAAGTTCTTTGGTAAAAACTTACCGTAAATGATTTCACTATTGTCAAACCTTTCCCTATCGATGATTT[C/T]
ATAAATGCTTCTAATGGTTTCACTTTCGATGATTTCACTATTGGCAAAAACTTGCAGTCAATAATTTCACTATCAATAAAAAGTTTTGATGTATTTATCA
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 | 96.20% | 3.60% | 0.25% | 0.00% | NA |
All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 92.50% | 6.80% | 0.73% | 0.00% | NA |
Aus | 269 | 99.30% | 0.70% | 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 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.60% | 0.10% | 0.26% | 0.00% | NA |
Tropical Japonica | 504 | 82.10% | 16.50% | 1.39% | 0.00% | NA |
Japonica Intermediate | 241 | 91.30% | 7.90% | 0.83% | 0.00% | NA |
VI/Aromatic | 96 | 46.90% | 53.10% | 0.00% | 0.00% | NA |
Intermediate | 90 | 87.80% | 11.10% | 1.11% | 0.00% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0107544024 | G -> A | LOC_Os01g13510.1 | missense_variant ; p.Met44Ile; MODERATE | nonsynonymous_codon ; M44I | Average:30.285; most accessible tissue: Callus, score: 55.379 | unknown | unknown | DELETERIOUS | 0.00 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0107544024 | 1.72E-06 | 1.72E-06 | mr1098 | 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 |
vg0107544024 | NA | 6.41E-06 | mr1101 | 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 |
vg0107544024 | 7.73E-08 | 7.73E-08 | mr1589 | 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 |
vg0107544024 | NA | 1.31E-06 | mr1961 | 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 |
vg0107544024 | NA | 1.83E-06 | mr1098_2 | 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 |
vg0107544024 | NA | 6.44E-06 | mr1150_2 | 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 |