Variant ID: vg0105869431 (JBrowse) | Variation Type: SNP |
Chromosome: chr01 | Position: 5869431 |
Reference Allele: G | Alternative Allele: C |
Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, C: 0.26, others allele: 0.00, population size: 90. )
TCTTTTTTAGCGCAAAGGGGGTTGAGAGGAGGCTTATTCACTCGCACCCCCACTCACCCCGTCCCTATCTCTCTTACCCTTTCAGCCTCTCCTCCCCTCC[G/C]
CTTGCCCCCTCTCCTCCACTCCACCTCTCCTCTCCGCGGCTCCCTCTCCATCGCCTGAGATGATGGCGAGAGCGGACGGAGCTGCATCCAGCAGTGGCGG
CCGCCACTGCTGGATGCAGCTCCGTCCGCTCTCGCCATCATCTCAGGCGATGGAGAGGGAGCCGCGGAGAGGAGAGGTGGAGTGGAGGAGAGGGGGCAAG[C/G]
GGAGGGGAGGAGAGGCTGAAAGGGTAAGAGAGATAGGGACGGGGTGAGTGGGGGTGCGAGTGAATAAGCCTCCTCTCAACCCCCTTTGCGCTAAAAAAGA
Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 75.70% | 24.30% | 0.00% | 0.00% | NA |
All Indica | 2759 | 69.10% | 30.90% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
Aus | 269 | 5.60% | 94.40% | 0.00% | 0.00% | NA |
Indica I | 595 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
Indica II | 465 | 60.40% | 39.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 46.10% | 53.90% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 77.90% | 22.10% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 97.90% | 2.10% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 83.30% | 16.70% | 0.00% | 0.00% | NA |
Intermediate | 90 | 80.00% | 20.00% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0105869431 | G -> C | LOC_Os01g11000.1 | missense_variant ; p.Arg18Gly; MODERATE | nonsynonymous_codon ; R18G | Average:63.335; most accessible tissue: Zhenshan97 young leaf, score: 77.736 | unknown | unknown | TOLERATED | 0.15 |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0105869431 | NA | 3.70E-06 | mr1236 | Ind_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 |
vg0105869431 | NA | 3.49E-06 | mr1496 | Ind_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 |
vg0105869431 | 1.93E-07 | 2.48E-13 | mr1498 | Ind_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 |
vg0105869431 | 6.75E-06 | NA | mr1769 | 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 |
vg0105869431 | 8.41E-07 | 1.42E-13 | mr1769 | Ind_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 |
vg0105869431 | 5.72E-07 | NA | mr1951 | 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 |
vg0105869431 | 4.55E-08 | 2.41E-12 | mr1951 | Ind_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 |
vg0105869431 | NA | 2.09E-07 | mr1582_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 |
vg0105869431 | NA | 3.60E-09 | mr1769_2 | Ind_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 |