| Variant ID: vg0610451701 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 10451701 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 85. )
ATATAACCCTTACCTTGTTACTATCCTCTTGCAAAATGCATGGATTGGTGAAATCATGTTTTTTGTCATGCAGAATCTATTATATTATTAAAACAGCCTT[A/G]
AAAAAAGACACCACGTTTGCTGTGGAGGCTAGAAATTTCCACATTAATCGAAGAAAAGGAAAAATATTTTAATCATTGGATCATAATAGATCTAGATTTT
AAAATCTAGATCTATTATGATCCAATGATTAAAATATTTTTCCTTTTCTTCGATTAATGTGGAAATTTCTAGCCTCCACAGCAAACGTGGTGTCTTTTTT[T/C]
AAGGCTGTTTTAATAATATAATAGATTCTGCATGACAAAAAACATGATTTCACCAATCCATGCATTTTGCAAGAGGATAGTAACAAGGTAAGGGTTATAT
| 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 | 31.90% | 2.10% | 4.70% | 61.26% | NA |
| All Indica | 2759 | 29.40% | 0.60% | 2.94% | 67.09% | NA |
| All Japonica | 1512 | 42.10% | 4.00% | 7.47% | 46.49% | NA |
| Aus | 269 | 4.10% | 5.20% | 7.81% | 82.90% | NA |
| Indica I | 595 | 14.60% | 1.30% | 2.52% | 81.51% | NA |
| Indica II | 465 | 15.70% | 0.00% | 0.65% | 83.66% | NA |
| Indica III | 913 | 38.10% | 0.80% | 4.16% | 56.96% | NA |
| Indica Intermediate | 786 | 38.40% | 0.30% | 3.18% | 58.14% | NA |
| Temperate Japonica | 767 | 54.20% | 3.90% | 6.39% | 35.46% | NA |
| Tropical Japonica | 504 | 31.90% | 3.80% | 8.73% | 55.56% | NA |
| Japonica Intermediate | 241 | 24.50% | 4.60% | 8.30% | 62.66% | NA |
| VI/Aromatic | 96 | 15.60% | 6.20% | 5.21% | 72.92% | NA |
| Intermediate | 90 | 40.00% | 4.40% | 2.22% | 53.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0610451701 | A -> G | LOC_Os06g17970.1 | downstream_gene_variant ; 549.0bp to feature; MODIFIER | silent_mutation | Average:44.389; most accessible tissue: Callus, score: 73.044 | N | N | N | N |
| vg0610451701 | A -> G | LOC_Os06g17980.1 | downstream_gene_variant ; 3052.0bp to feature; MODIFIER | silent_mutation | Average:44.389; most accessible tissue: Callus, score: 73.044 | N | N | N | N |
| vg0610451701 | A -> G | LOC_Os06g17970-LOC_Os06g17980 | intergenic_region ; MODIFIER | silent_mutation | Average:44.389; most accessible tissue: Callus, score: 73.044 | N | N | N | N |
| vg0610451701 | A -> DEL | N | N | silent_mutation | Average:44.389; most accessible tissue: Callus, score: 73.044 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0610451701 | 3.00E-06 | NA | mr1065 | 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 |
| vg0610451701 | 1.39E-08 | 2.26E-12 | mr1065 | 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 |
| vg0610451701 | 2.60E-06 | 1.51E-09 | mr1067 | 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 |
| vg0610451701 | 3.22E-12 | NA | mr1068 | 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 |
| vg0610451701 | 5.50E-13 | 2.67E-18 | mr1068 | 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 |
| vg0610451701 | 1.12E-06 | NA | mr1078 | 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 |
| vg0610451701 | NA | 1.48E-07 | mr1078 | 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 |
| vg0610451701 | 1.33E-07 | NA | mr1087 | 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 |
| vg0610451701 | 1.30E-16 | 7.35E-24 | mr1087 | 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 |
| vg0610451701 | 2.81E-14 | NA | mr1090 | 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 |
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