| Variant ID: vg0407010552 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 7010552 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TGGGCAATATTAGAATGTCTTATAATATGAAACGGAGGGAGTATAGAAAAGGAAATTTGTGCTGGTTGGGAGATGACCATAGGTGCCAGATTTTCCAACG[C/G]
CACCCAGCAAAGCAACACCTTTGAGGTCCCAGGAATGAAAAAAAACTGGCTTGATGCCTTGACCAACTCTCCGTCATCACTGAGATCACCATCATTCACA
TGTGAATGATGGTGATCTCAGTGATGACGGAGAGTTGGTCAAGGCATCAAGCCAGTTTTTTTTCATTCCTGGGACCTCAAAGGTGTTGCTTTGCTGGGTG[G/C]
CGTTGGAAAATCTGGCACCTATGGTCATCTCCCAACCAGCACAAATTTCCTTTTCTATACTCCCTCCGTTTCATATTATAAGACATTCTAATATTGCCCA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 59.60% | 14.20% | 0.38% | 25.90% | NA |
| All Indica | 2759 | 56.00% | 5.50% | 0.36% | 38.13% | NA |
| All Japonica | 1512 | 66.70% | 32.30% | 0.26% | 0.73% | NA |
| Aus | 269 | 59.90% | 0.00% | 0.74% | 39.41% | NA |
| Indica I | 595 | 77.30% | 0.00% | 0.34% | 22.35% | NA |
| Indica II | 465 | 32.00% | 20.90% | 0.22% | 46.88% | NA |
| Indica III | 913 | 57.70% | 2.80% | 0.33% | 39.10% | NA |
| Indica Intermediate | 786 | 52.00% | 3.70% | 0.51% | 43.77% | NA |
| Temperate Japonica | 767 | 97.90% | 1.80% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 16.10% | 82.30% | 0.40% | 1.19% | NA |
| Japonica Intermediate | 241 | 73.00% | 24.90% | 0.41% | 1.66% | NA |
| VI/Aromatic | 96 | 52.10% | 15.60% | 0.00% | 32.29% | NA |
| Intermediate | 90 | 56.70% | 14.40% | 2.22% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0407010552 | C -> DEL | N | N | silent_mutation | Average:6.868; most accessible tissue: Callus, score: 26.923 | N | N | N | N |
| vg0407010552 | C -> G | LOC_Os04g12639.1 | upstream_gene_variant ; 4920.0bp to feature; MODIFIER | silent_mutation | Average:6.868; most accessible tissue: Callus, score: 26.923 | N | N | N | N |
| vg0407010552 | C -> G | LOC_Os04g12660.1 | downstream_gene_variant ; 464.0bp to feature; MODIFIER | silent_mutation | Average:6.868; most accessible tissue: Callus, score: 26.923 | N | N | N | N |
| vg0407010552 | C -> G | LOC_Os04g12669.1 | downstream_gene_variant ; 3790.0bp to feature; MODIFIER | silent_mutation | Average:6.868; most accessible tissue: Callus, score: 26.923 | N | N | N | N |
| vg0407010552 | C -> G | LOC_Os04g12660-LOC_Os04g12669 | intergenic_region ; MODIFIER | silent_mutation | Average:6.868; most accessible tissue: Callus, score: 26.923 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0407010552 | NA | 4.97E-07 | mr1157 | 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 |
| vg0407010552 | NA | 4.33E-06 | mr1192 | 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 |
| vg0407010552 | NA | 1.14E-08 | mr1593 | 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 |
| vg0407010552 | NA | 1.50E-07 | mr1608 | 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 |
| vg0407010552 | NA | 6.02E-06 | mr1835 | 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 |
| vg0407010552 | NA | 8.00E-08 | mr1835 | 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 |
| vg0407010552 | NA | 2.56E-06 | mr1121_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 |
| vg0407010552 | NA | 3.94E-06 | mr1211_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 |
| vg0407010552 | NA | 9.12E-08 | mr1526_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 |
| vg0407010552 | NA | 5.75E-13 | mr1593_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 |
| vg0407010552 | NA | 4.48E-08 | mr1830_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 |
| vg0407010552 | NA | 1.11E-14 | mr1846_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 |