| Variant ID: vg0906202716 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 6202716 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGTTTAATAATAGAGCCAACTATGAGCTTATAGCTTATATTAAATAGTTTCCCTGAAAAAAAAAGCTTATATTAAATAGTTAACATATATAATAAGTGAG[C/T]
TACAAGGTTATCTTTTTTTTCTCATCCTCTCTCTATCTCTCACCTATGCATTTAATGTATTTATCTTGAACTATGTGAATAGCTAGTTCTTGTATGAGAG
CTCTCATACAAGAACTAGCTATTCACATAGTTCAAGATAAATACATTAAATGCATAGGTGAGAGATAGAGAGAGGATGAGAAAAAAAAGATAACCTTGTA[G/A]
CTCACTTATTATATATGTTAACTATTTAATATAAGCTTTTTTTTTCAGGGAAACTATTTAATATAAGCTATAAGCTCATAGTTGGCTCTATTATTAAACT
| 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 | 66.60% | 4.80% | 0.34% | 28.27% | NA |
| All Indica | 2759 | 65.40% | 5.00% | 0.29% | 29.32% | NA |
| All Japonica | 1512 | 73.50% | 5.20% | 0.20% | 21.16% | NA |
| Aus | 269 | 57.60% | 0.40% | 0.37% | 41.64% | NA |
| Indica I | 595 | 84.20% | 11.60% | 0.34% | 3.87% | NA |
| Indica II | 465 | 41.90% | 0.20% | 0.43% | 57.42% | NA |
| Indica III | 913 | 68.50% | 3.50% | 0.00% | 28.04% | NA |
| Indica Intermediate | 786 | 61.60% | 4.50% | 0.51% | 33.46% | NA |
| Temperate Japonica | 767 | 85.80% | 3.00% | 0.26% | 10.95% | NA |
| Tropical Japonica | 504 | 68.80% | 8.90% | 0.20% | 22.02% | NA |
| Japonica Intermediate | 241 | 44.00% | 4.10% | 0.00% | 51.87% | NA |
| VI/Aromatic | 96 | 10.40% | 9.40% | 3.12% | 77.08% | NA |
| Intermediate | 90 | 72.20% | 3.30% | 1.11% | 23.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0906202716 | C -> DEL | N | N | silent_mutation | Average:45.028; most accessible tissue: Callus, score: 96.264 | N | N | N | N |
| vg0906202716 | C -> T | LOC_Os09g11190.1 | upstream_gene_variant ; 2927.0bp to feature; MODIFIER | silent_mutation | Average:45.028; most accessible tissue: Callus, score: 96.264 | N | N | N | N |
| vg0906202716 | C -> T | LOC_Os09g11180.1 | downstream_gene_variant ; 4885.0bp to feature; MODIFIER | silent_mutation | Average:45.028; most accessible tissue: Callus, score: 96.264 | N | N | N | N |
| vg0906202716 | C -> T | LOC_Os09g11180-LOC_Os09g11190 | intergenic_region ; MODIFIER | silent_mutation | Average:45.028; most accessible tissue: Callus, score: 96.264 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0906202716 | 5.23E-07 | 5.24E-07 | mr1389 | 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 |
| vg0906202716 | 2.40E-07 | 1.61E-08 | mr1038_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 |
| vg0906202716 | 4.33E-09 | 4.33E-09 | mr1389_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 |