Variant ID: vg0321868776 (JBrowse) | Variation Type: SNP |
Chromosome: chr03 | Position: 21868776 |
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: 104. )
AGCAGCCTCTGCAACCGATCCAACAGACTACGTTAAGGCAGCAAATCATTCAGCCGATTCAGCAACAGGGGTCTGTAAGCGCATCGGCCGGGTTCGCAGC[G/A]
CCTAGAGGTCAGCCTATACAACAATTTGTAAACCAAGTCATCCCAGAACATTTGGTTCACCACGTACAGCCGGACGGCACAGTAATGCCTTAGGTTGTTC
GAACAACCTAAGGCATTACTGTGCCGTCCGGCTGTACGTGGTGAACCAAATGTTCTGGGATGACTTGGTTTACAAATTGTTGTATAGGCTGACCTCTAGG[C/T]
GCTGCGAACCCGGCCGATGCGCTTACAGACCCCTGTTGCTGAATCGGCTGAATGATTTGCTGCCTTAACGTAGTCTGTTGGATCGGTTGCAGAGGCTGCT
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 | 47.40% | 18.70% | 4.42% | 29.50% | NA |
All Indica | 2759 | 20.40% | 29.50% | 3.70% | 46.39% | NA |
All Japonica | 1512 | 98.30% | 0.10% | 0.00% | 1.59% | NA |
Aus | 269 | 12.30% | 23.00% | 38.29% | 26.39% | NA |
Indica I | 595 | 25.90% | 58.00% | 2.18% | 13.95% | NA |
Indica II | 465 | 29.50% | 12.00% | 2.37% | 56.13% | NA |
Indica III | 913 | 4.10% | 29.70% | 4.82% | 61.45% | NA |
Indica Intermediate | 786 | 30.00% | 17.90% | 4.33% | 47.71% | NA |
Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
Tropical Japonica | 504 | 95.40% | 0.00% | 0.00% | 4.56% | NA |
Japonica Intermediate | 241 | 99.60% | 0.00% | 0.00% | 0.41% | NA |
VI/Aromatic | 96 | 96.90% | 0.00% | 1.04% | 2.08% | NA |
Intermediate | 90 | 68.90% | 8.90% | 3.33% | 18.89% | NA |
Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
---|---|---|---|---|---|---|---|---|---|
vg0321868776 | G -> A | LOC_Os03g39350.1 | intron_variant ; MODIFIER | silent_mutation | Average:66.325; most accessible tissue: Minghui63 young leaf, score: 79.191 | N | N | N | N |
vg0321868776 | G -> DEL | N | N | silent_mutation | Average:66.325; most accessible tissue: Minghui63 young leaf, score: 79.191 | N | N | N | N |
Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
---|---|---|---|---|---|---|
vg0321868776 | NA | 1.61E-20 | mr1689 | 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 |
vg0321868776 | 3.76E-06 | NA | mr1718 | 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 |
vg0321868776 | 3.26E-06 | 2.46E-09 | mr1718 | 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 |
vg0321868776 | 7.65E-07 | NA | mr1750 | 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 |
vg0321868776 | 4.84E-06 | 1.62E-11 | mr1750 | 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 |
vg0321868776 | NA | 2.06E-16 | mr1842 | 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 |
vg0321868776 | NA | 2.76E-07 | mr1850 | 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 |
vg0321868776 | NA | 8.28E-07 | mr1568_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 |
vg0321868776 | 1.27E-08 | NA | mr1718_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 |
vg0321868776 | 2.03E-08 | 4.69E-10 | mr1718_2 | 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 |