| Variant ID: vg1002656443 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 2656443 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
GTGGCCGTCCCCCGCCCAGATCCAGCGGTGGCTGGCCAGCAGGCGTTTTGCTATTTTTATTTTTGTGTGTGGACGACATAAACATCCGCACACGGAAATC[C/T]
GATTTTCGCATGTGGGTGCGCCACCCTCATAGAAAAATAGAGATTTTCATAGACATTTCTGGGCAAACGGCCCGGAGGTCCGCAAGCAAAAATCACTTTT
AAAAGTGATTTTTGCTTGCGGACCTCCGGGCCGTTTGCCCAGAAATGTCTATGAAAATCTCTATTTTTCTATGAGGGTGGCGCACCCACATGCGAAAATC[G/A]
GATTTCCGTGTGCGGATGTTTATGTCGTCCACACACAAAAATAAAAATAGCAAAACGCCTGCTGGCCAGCCACCGCTGGATCTGGGCGGGGGACGGCCAC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 55.90% | 40.40% | 0.23% | 3.47% | NA |
| All Indica | 2759 | 91.30% | 8.20% | 0.14% | 0.36% | NA |
| All Japonica | 1512 | 5.50% | 85.10% | 0.46% | 8.99% | NA |
| Aus | 269 | 0.70% | 96.30% | 0.00% | 2.97% | NA |
| Indica I | 595 | 99.00% | 0.50% | 0.50% | 0.00% | NA |
| Indica II | 465 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 85.90% | 13.30% | 0.00% | 0.88% | NA |
| Indica Intermediate | 786 | 88.20% | 11.50% | 0.13% | 0.25% | NA |
| Temperate Japonica | 767 | 7.40% | 79.90% | 0.65% | 11.99% | NA |
| Tropical Japonica | 504 | 3.00% | 93.50% | 0.00% | 3.57% | NA |
| Japonica Intermediate | 241 | 4.60% | 83.80% | 0.83% | 10.79% | NA |
| VI/Aromatic | 96 | 3.10% | 88.50% | 0.00% | 8.33% | NA |
| Intermediate | 90 | 40.00% | 57.80% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1002656443 | C -> T | LOC_Os10g05380.1 | upstream_gene_variant ; 2018.0bp to feature; MODIFIER | silent_mutation | Average:62.798; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 | N | N | N | N |
| vg1002656443 | C -> T | LOC_Os10g05390.1 | upstream_gene_variant ; 904.0bp to feature; MODIFIER | silent_mutation | Average:62.798; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 | N | N | N | N |
| vg1002656443 | C -> T | LOC_Os10g05380-LOC_Os10g05390 | intergenic_region ; MODIFIER | silent_mutation | Average:62.798; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 | N | N | N | N |
| vg1002656443 | C -> DEL | N | N | silent_mutation | Average:62.798; most accessible tissue: Zhenshan97 flag leaf, score: 75.455 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1002656443 | 2.55E-06 | NA | mr1942 | 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 |
| vg1002656443 | NA | 7.77E-06 | mr1968 | 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 |
| vg1002656443 | NA | 7.34E-08 | mr1321_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 |
| vg1002656443 | NA | 3.17E-12 | mr1666_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 |
| vg1002656443 | NA | 4.37E-10 | mr1761_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 |