| Variant ID: vg0802041179 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 2041179 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TTAGTTGACCGTTAAATTCTTTTGAAAAAGTCCATTTTGCCCTTTCCTATGAAGAAACATAATAAATTAATGAAGTACATTGTTGGAATGTAAAAATTTA[C/T]
TGGATGAGACTATTATATTTATGAGTCTGTGATGCACCATATTATTTGTGACAAATTTACTTTTACATATGATATAAAAATTTAATACTTATTTATTAGT
ACTAATAAATAAGTATTAAATTTTTATATCATATGTAAAAGTAAATTTGTCACAAATAATATGGTGCATCACAGACTCATAAATATAATAGTCTCATCCA[G/A]
TAAATTTTTACATTCCAACAATGTACTTCATTAATTTATTATGTTTCTTCATAGGAAAGGGCAAAATGGACTTTTTCAAAAGAATTTAACGGTCAACTAA
| 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 | 57.60% | 42.30% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 78.70% | 21.30% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 15.60% | 84.40% | 0.00% | 0.00% | NA |
| Aus | 269 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.70% | 1.30% | 0.00% | 0.00% | NA |
| Indica II | 465 | 84.10% | 15.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 67.70% | 32.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 73.00% | 26.80% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 2.60% | 97.40% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 40.10% | 59.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 5.80% | 94.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 6.20% | 93.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 50.00% | 48.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0802041179 | C -> T | LOC_Os08g04190.1 | upstream_gene_variant ; 3675.0bp to feature; MODIFIER | silent_mutation | Average:22.687; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0802041179 | C -> T | LOC_Os08g04200.1 | downstream_gene_variant ; 1371.0bp to feature; MODIFIER | silent_mutation | Average:22.687; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0802041179 | C -> T | LOC_Os08g04190-LOC_Os08g04200 | intergenic_region ; MODIFIER | silent_mutation | Average:22.687; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0802041179 | NA | 6.78E-09 | mr1198 | 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 |
| vg0802041179 | NA | 8.19E-14 | mr1653 | 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 |
| vg0802041179 | 4.37E-07 | NA | mr1739_2 | 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 |