Variant ID: vg0413666850 (JBrowse) | Variation Type: SNP |
Chromosome: chr04 | Position: 13666850 |
Reference Allele: G | Alternative Allele: A |
Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 173. )
TGGGTAGATGGTGAGGCTGTTGGAGCGAGTAACTAGTTTGACTAGCCAAATCAGATGGAAAGTTAGCTATGTGGGTGTTTGGAGAGTCCGATTTAGATAT[G/A]
CTGTTGAAGATGCTCTTAATCTTTGTCAATTGGGTCAATTAACATGCATGCCAGAAAGAAATTAAACCTAAGGTTTTTTTTTGTTTTATTCGTCCTAATG
CATTAGGACGAATAAAACAAAAAAAAACCTTAGGTTTAATTTCTTTCTGGCATGCATGTTAATTGACCCAATTGACAAAGATTAAGAGCATCTTCAACAG[C/T]
ATATCTAAATCGGACTCTCCAAACACCCACATAGCTAACTTTCCATCTGATTTGGCTAGTCAAACTAGTTACTCGCTCCAACAGCCTCACCATCTACCCA
Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
---|---|---|---|---|---|---|
All | 4726 | 68.80% | 31.20% | 0.02% | 0.00% | NA |
All Indica | 2759 | 97.00% | 3.00% | 0.00% | 0.00% | NA |
All Japonica | 1512 | 11.80% | 88.20% | 0.00% | 0.00% | NA |
Aus | 269 | 94.40% | 5.60% | 0.00% | 0.00% | NA |
Indica I | 595 | 97.50% | 2.50% | 0.00% | 0.00% | NA |
Indica II | 465 | 97.40% | 2.60% | 0.00% | 0.00% | NA |
Indica III | 913 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
Indica Intermediate | 786 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
Temperate Japonica | 767 | 2.00% | 98.00% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 18.10% | 81.90% | 0.00% | 0.00% | NA |
Japonica Intermediate | 241 | 30.30% | 69.70% | 0.00% | 0.00% | NA |
VI/Aromatic | 96 | 87.50% | 12.50% | 0.00% | 0.00% | NA |
Intermediate | 90 | 62.20% | 36.70% | 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 |
---|---|---|---|---|---|---|---|---|---|
vg0413666850 | G -> A | LOC_Os04g23890-LOC_Os04g23910 | intergenic_region ; MODIFIER | silent_mutation | Average:58.763; most accessible tissue: Minghui63 root, score: 72.958 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0413666850 | NA | 5.79E-36 | mr1350 | 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 |
vg0413666850 | NA | 5.69E-06 | mr1866 | 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 |
vg0413666850 | 3.10E-06 | 4.63E-31 | mr1350_2 | 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 |
vg0413666850 | 3.24E-06 | 7.07E-11 | mr1350_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 |
vg0413666850 | 9.54E-06 | 1.38E-18 | mr1730_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 |
vg0413666850 | 4.36E-07 | 1.34E-08 | mr1730_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 |
vg0413666850 | NA | 7.06E-16 | mr1866_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 |
vg0413666850 | NA | 4.85E-06 | mr1866_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 |