| Variant ID: vg0809647546 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 9647546 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGCACGAAACACGCAAGCGAAGAGGAAGGCGAGCCGTCGCGAACGAACAGGGAGCAGTCGCGCGAAGCGCTTCCCAAAAACCTTATTGCCGCCTTCTCC[C/T]
GGTGCAAGACGTCGAAGGCAGAGGTTCCGGAGACCTGCTCTCCCGATCGCCGGTGCACGCCGGTGAGCGGGATGGAGTAGTCTACGAGCGACGGCGCAGT
ACTGCGCCGTCGCTCGTAGACTACTCCATCCCGCTCACCGGCGTGCACCGGCGATCGGGAGAGCAGGTCTCCGGAACCTCTGCCTTCGACGTCTTGCACC[G/A]
GGAGAAGGCGGCAATAAGGTTTTTGGGAAGCGCTTCGCGCGACTGCTCCCTGTTCGTTCGCGACGGCTCGCCTTCCTCTTCGCTTGCGTGTTTCGTGCCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.10% | 6.70% | 3.09% | 7.07% | NA |
| All Indica | 2759 | 89.10% | 6.40% | 2.03% | 2.50% | NA |
| All Japonica | 1512 | 81.40% | 0.10% | 4.70% | 13.82% | NA |
| Aus | 269 | 46.50% | 52.00% | 0.74% | 0.74% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 60.20% | 26.00% | 4.95% | 8.82% | NA |
| Indica III | 913 | 95.60% | 0.70% | 2.52% | 1.20% | NA |
| Indica Intermediate | 786 | 90.30% | 6.20% | 1.27% | 2.16% | NA |
| Temperate Japonica | 767 | 91.00% | 0.00% | 6.52% | 2.48% | NA |
| Tropical Japonica | 504 | 66.10% | 0.00% | 3.17% | 30.75% | NA |
| Japonica Intermediate | 241 | 83.00% | 0.40% | 2.07% | 14.52% | NA |
| VI/Aromatic | 96 | 37.50% | 0.00% | 14.58% | 47.92% | NA |
| Intermediate | 90 | 85.60% | 2.20% | 3.33% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0809647546 | C -> T | LOC_Os08g15860.1 | upstream_gene_variant ; 908.0bp to feature; MODIFIER | silent_mutation | Average:33.723; most accessible tissue: Zhenshan97 root, score: 60.612 | N | N | N | N |
| vg0809647546 | C -> T | LOC_Os08g15870.1 | downstream_gene_variant ; 873.0bp to feature; MODIFIER | silent_mutation | Average:33.723; most accessible tissue: Zhenshan97 root, score: 60.612 | N | N | N | N |
| vg0809647546 | C -> T | LOC_Os08g15860-LOC_Os08g15870 | intergenic_region ; MODIFIER | silent_mutation | Average:33.723; most accessible tissue: Zhenshan97 root, score: 60.612 | N | N | N | N |
| vg0809647546 | C -> DEL | N | N | silent_mutation | Average:33.723; most accessible tissue: Zhenshan97 root, score: 60.612 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0809647546 | NA | 9.50E-06 | mr1076 | 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 |
| vg0809647546 | NA | 5.63E-08 | mr1082 | 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 |
| vg0809647546 | NA | 2.98E-08 | mr1411 | 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 |
| vg0809647546 | NA | 1.94E-06 | mr1560 | 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 |