Variant ID: vg0330420931 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 30420931 |
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: 250. )
CTCCACATCATTAAGAAACTAGTATTAGACACTACTCTCCCAATGCAAACACCACTATTCCATACTTAAATTAAATGCTACTTACCTCACATAATGTCTT[G/A]
GATGTTGTGTAGAAATCATGTCTCATGCAAGACTCTTTTATCATTTATTCACTTGCCACATCATTTTTCATTCTAGGTGACAGCTTATTTAATGCTATGG
CCATAGCATTAAATAAGCTGTCACCTAGAATGAAAAATGATGTGGCAAGTGAATAAATGATAAAAGAGTCTTGCATGAGACATGATTTCTACACAACATC[C/T]
AAGACATTATGTGAGGTAAGTAGCATTTAATTTAAGTATGGAATAGTGGTGTTTGCATTGGGAGAGTAGTGTCTAATACTAGTTTCTTAATGATGTGGAG
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 | 93.60% | 5.60% | 0.76% | 0.00% | NA |
All Indica | 2759 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 85.60% | 12.10% | 2.31% | 0.00% | NA |
Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Indica III | 913 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 94.00% | 2.90% | 3.13% | 0.00% | NA |
Tropical Japonica | 504 | 89.50% | 10.30% | 0.20% | 0.00% | NA |
Japonica Intermediate | 241 | 50.60% | 45.20% | 4.15% | 0.00% | NA |
VI/Aromatic | 96 | 19.80% | 79.20% | 1.04% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0330420931 | G -> A | LOC_Os03g53050.1 | upstream_gene_variant ; 1260.0bp to feature; MODIFIER | silent_mutation | Average:56.766; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
vg0330420931 | G -> A | LOC_Os03g53030-LOC_Os03g53050 | intergenic_region ; MODIFIER | silent_mutation | Average:56.766; most accessible tissue: Minghui63 flag leaf, score: 73.334 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0330420931 | 7.77E-06 | NA | mr1274 | 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 |
vg0330420931 | 3.83E-06 | 1.19E-10 | mr1281 | 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 |
vg0330420931 | 3.29E-06 | NA | mr1842_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 |
vg0330420931 | 6.77E-06 | 2.34E-09 | mr1947_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 |