| Variant ID: vg0134766241 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 34766241 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TCATGATTTTCTAAAAATATATATATCCAAGCAAACTCCCACAGTGAATTTCATCTTAACTAAACCATATAACAATAATAAGATTAAAATAGACTTCACC[T/C]
ATTGCAACGCACGAGCATTTTTTCTAGTAGAAATAAAATTTCAGAGTTGTATATTAAATCTAAGGCTTGTTTGGCATGGGTCTAGTTTCAACTCCATCTC
GAGATGGAGTTGAAACTAGACCCATGCCAAACAAGCCTTAGATTTAATATACAACTCTGAAATTTTATTTCTACTAGAAAAAATGCTCGTGCGTTGCAAT[A/G]
GGTGAAGTCTATTTTAATCTTATTATTGTTATATGGTTTAGTTAAGATGAAATTCACTGTGGGAGTTTGCTTGGATATATATATTTTTAGAAAATCATGA
| 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 | 77.60% | 22.40% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 39.70% | 60.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 46.40% | 53.60% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 41.30% | 58.70% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 14.90% | 85.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 10.40% | 89.60% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 54.40% | 45.60% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0134766241 | T -> C | LOC_Os01g60110.1 | downstream_gene_variant ; 2876.0bp to feature; MODIFIER | silent_mutation | Average:33.612; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg0134766241 | T -> C | LOC_Os01g60100-LOC_Os01g60110 | intergenic_region ; MODIFIER | silent_mutation | Average:33.612; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0134766241 | 2.62E-06 | NA | mr1019_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 |
| vg0134766241 | NA | 3.63E-08 | mr1084_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 |
| vg0134766241 | NA | 1.61E-07 | mr1205_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 |
| vg0134766241 | 4.91E-07 | NA | mr1261_2 | 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 |