| Variant ID: vg0809822175 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9822175 |
| Reference Allele: A | Alternative Allele: T,G |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 90. )
AATTACTAGCAAATATATGCTTTGTGTTACTTATATCTATTACTTATATTAGTATATATTAATATTCGAAAAAGTGCCTCTACATAGGCTTAAATGCCTC[A/T,G]
AGAAAATGCCTTTACATATGAGGCAAATTTCAAAGTGTTGGAAAAATGTCTCTACAAGATAAAATTAACAAAATATGCTAAGAGTGTCTCTAGAGTAAAA
TTTTACTCTAGAGACACTCTTAGCATATTTTGTTAATTTTATCTTGTAGAGACATTTTTCCAACACTTTGAAATTTGCCTCATATGTAAAGGCATTTTCT[T/A,C]
GAGGCATTTAAGCCTATGTAGAGGCACTTTTTCGAATATTAATATATACTAATATAAGTAATAGATATAAGTAACACAAAGCATATATTTGCTAGTAATT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 60.90% | 39.00% | 0.11% | 0.00% | NA |
| All Indica | 2759 | 58.80% | 41.10% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 64.40% | 35.40% | 0.20% | 0.00% | NA |
| Aus | 269 | 48.30% | 51.30% | 0.37% | 0.00% | NA |
| Indica I | 595 | 60.30% | 39.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 70.80% | 29.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 47.30% | 52.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 64.00% | 36.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 88.40% | 11.20% | 0.39% | 0.00% | NA |
| Tropical Japonica | 504 | 38.30% | 61.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 42.30% | 57.70% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 93.80% | 6.20% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 70.00% | 30.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0809822175 | A -> G | LOC_Os08g16100.1 | upstream_gene_variant ; 3773.0bp to feature; MODIFIER | N | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> G | LOC_Os08g16110.1 | upstream_gene_variant ; 555.0bp to feature; MODIFIER | N | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> G | LOC_Os08g16120.1 | upstream_gene_variant ; 2452.0bp to feature; MODIFIER | N | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> G | LOC_Os08g16120.2 | upstream_gene_variant ; 2452.0bp to feature; MODIFIER | N | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> G | LOC_Os08g16110-LOC_Os08g16120 | intergenic_region ; MODIFIER | N | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> T | LOC_Os08g16100.1 | upstream_gene_variant ; 3773.0bp to feature; MODIFIER | silent_mutation | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> T | LOC_Os08g16110.1 | upstream_gene_variant ; 555.0bp to feature; MODIFIER | silent_mutation | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> T | LOC_Os08g16120.1 | upstream_gene_variant ; 2452.0bp to feature; MODIFIER | silent_mutation | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> T | LOC_Os08g16120.2 | upstream_gene_variant ; 2452.0bp to feature; MODIFIER | silent_mutation | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| vg0809822175 | A -> T | LOC_Os08g16110-LOC_Os08g16120 | intergenic_region ; MODIFIER | silent_mutation | Average:44.384; most accessible tissue: Minghui63 root, score: 77.009 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809822175 | NA | 7.13E-06 | mr1063 | 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 |
| vg0809822175 | NA | 1.48E-07 | mr1164 | Jap_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 |
| vg0809822175 | NA | 3.11E-08 | mr1864 | 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 |
| vg0809822175 | NA | 5.12E-07 | mr1194_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 |
| vg0809822175 | NA | 5.27E-06 | mr1482_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 |