| Variant ID: vg0226040606 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 26040606 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GTAATGGTCGATACTAATTACTCCCTCTATATAACTATCAAAAGTAGATTGAGGGATTACTATTTTTACTTATTTTCTGTTTAAAGTTTTAAAATTTTGA[C/T]
TGCCGCATATTTTAACGGAGCCATCATTTTGCTTATTCGCGGAATAAGCGAAACGGCATATTTGAAAATAAAAGGTAATTTGTAAATAAAATTTTTATAT
ATATAAAAATTTTATTTACAAATTACCTTTTATTTTCAAATATGCCGTTTCGCTTATTCCGCGAATAAGCAAAATGATGGCTCCGTTAAAATATGCGGCA[G/A]
TCAAAATTTTAAAACTTTAAACAGAAAATAAGTAAAAATAGTAATCCCTCAATCTACTTTTGATAGTTATATAGAGGGAGTAATTAGTATCGACCATTAC
| 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 | 94.60% | 2.60% | 2.84% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.00% | 0.29% | 0.00% | NA |
| All Japonica | 1512 | 83.70% | 8.00% | 8.27% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.10% | 0.00% | 0.89% | 0.00% | NA |
| Temperate Japonica | 767 | 70.40% | 14.70% | 14.86% | 0.00% | NA |
| Tropical Japonica | 504 | 98.20% | 1.20% | 0.60% | 0.00% | NA |
| Japonica Intermediate | 241 | 95.90% | 0.80% | 3.32% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0226040606 | C -> T | LOC_Os02g43210.1 | upstream_gene_variant ; 1754.0bp to feature; MODIFIER | silent_mutation | Average:23.611; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0226040606 | C -> T | LOC_Os02g43194.1 | intron_variant ; MODIFIER | silent_mutation | Average:23.611; 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 |
|---|---|---|---|---|---|---|
| vg0226040606 | NA | 6.34E-06 | mr1221_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 |
| vg0226040606 | 4.97E-07 | 4.97E-07 | mr1908_2 | 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 |
| vg0226040606 | NA | 4.17E-06 | mr1996_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 |