| Variant ID: vg0620354393 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20354393 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
CAACGGGAGAGCTCGGTCTCTTGAAGGCACGACGCCTTTTTCAAGATGACGGGAAGGCCGCGCCGCCGAGCGCTATGTGGACACCCTCTTCACCAAGGCA[A/G]
GGGATGAGGTGCTCCACAAGTACACCACACCCACCGCTACTCCATCTACTCCGAAGGAGGAGCGATTCCGTATTCAGGGAGTGCGAACTCCCGGCGGTGG
CCACCGCCGGGAGTTCGCACTCCCTGAATACGGAATCGCTCCTCCTTCGGAGTAGATGGAGTAGCGGTGGGTGTGGTGTACTTGTGGAGCACCTCATCCC[T/C]
TGCCTTGGTGAAGAGGGTGTCCACATAGCGCTCGGCGGCGCGGCCTTCCCGTCATCTTGAAAAAGGCGTCGTGCCTTCAAGAGACCGAGCTCTCCCGTTG
| 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 | 36.90% | 1.00% | 4.76% | 57.36% | NA |
| All Indica | 2759 | 8.40% | 1.60% | 7.03% | 82.89% | NA |
| All Japonica | 1512 | 92.90% | 0.00% | 0.07% | 7.01% | NA |
| Aus | 269 | 4.80% | 0.00% | 5.58% | 89.59% | NA |
| Indica I | 595 | 15.50% | 3.50% | 8.24% | 72.77% | NA |
| Indica II | 465 | 8.20% | 0.20% | 2.58% | 89.03% | NA |
| Indica III | 913 | 1.50% | 2.00% | 6.46% | 90.03% | NA |
| Indica Intermediate | 786 | 11.30% | 0.60% | 9.41% | 78.63% | NA |
| Temperate Japonica | 767 | 93.70% | 0.00% | 0.13% | 6.13% | NA |
| Tropical Japonica | 504 | 93.70% | 0.00% | 0.00% | 6.35% | NA |
| Japonica Intermediate | 241 | 88.80% | 0.00% | 0.00% | 11.20% | NA |
| VI/Aromatic | 96 | 46.90% | 0.00% | 11.46% | 41.67% | NA |
| Intermediate | 90 | 53.30% | 1.10% | 4.44% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620354393 | A -> G | LOC_Os06g34990.1 | upstream_gene_variant ; 4829.0bp to feature; MODIFIER | silent_mutation | Average:23.461; most accessible tissue: Zhenshan97 root, score: 43.05 | N | N | N | N |
| vg0620354393 | A -> G | LOC_Os06g35000.1 | downstream_gene_variant ; 1054.0bp to feature; MODIFIER | silent_mutation | Average:23.461; most accessible tissue: Zhenshan97 root, score: 43.05 | N | N | N | N |
| vg0620354393 | A -> G | LOC_Os06g35000-LOC_Os06g35010 | intergenic_region ; MODIFIER | silent_mutation | Average:23.461; most accessible tissue: Zhenshan97 root, score: 43.05 | N | N | N | N |
| vg0620354393 | A -> DEL | N | N | silent_mutation | Average:23.461; most accessible tissue: Zhenshan97 root, score: 43.05 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0620354393 | 9.65E-07 | 1.75E-06 | mr1719 | 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 |
| vg0620354393 | 3.74E-06 | 1.60E-06 | mr1856 | 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 |
| vg0620354393 | NA | 8.61E-17 | mr1342_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 |