| Variant ID: vg0827004405 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 27004405 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCCAACCGTAAATCCGATTGACTCCGTTCAACTTCCAAAATTCCTCAAATCTCGAGATCTATCTAATGGCACGCTTAGAGGTCATTAATAGGGCTTTATT[C/T]
TCGCCGTTTGTTGAGTTGTCCCGTTTCGCGTGTAGTTTCGGAGCCCGAAGACCCGCAGTGCGAGGATTTCGAGGATCAAGCTCCGGATCTCGAGCAAGGC
GCCTTGCTCGAGATCCGGAGCTTGATCCTCGAAATCCTCGCACTGCGGGTCTTCGGGCTCCGAAACTACACGCGAAACGGGACAACTCAACAAACGGCGA[G/A]
AATAAAGCCCTATTAATGACCTCTAAGCGTGCCATTAGATAGATCTCGAGATTTGAGGAATTTTGGAAGTTGAACGGAGTCAATCGGATTTACGGTTGGG
| 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 | 31.60% | 0.20% | 5.18% | 63.06% | NA |
| All Indica | 2759 | 2.50% | 0.30% | 8.08% | 89.16% | NA |
| All Japonica | 1512 | 86.70% | 0.00% | 0.60% | 12.70% | NA |
| Aus | 269 | 1.90% | 0.00% | 4.46% | 93.68% | NA |
| Indica I | 595 | 2.20% | 0.30% | 1.01% | 96.47% | NA |
| Indica II | 465 | 2.40% | 0.20% | 5.38% | 92.04% | NA |
| Indica III | 913 | 2.00% | 0.10% | 13.47% | 84.45% | NA |
| Indica Intermediate | 786 | 3.40% | 0.40% | 8.78% | 87.40% | NA |
| Temperate Japonica | 767 | 94.40% | 0.00% | 0.00% | 5.61% | NA |
| Tropical Japonica | 504 | 75.40% | 0.00% | 1.79% | 22.82% | NA |
| Japonica Intermediate | 241 | 85.90% | 0.00% | 0.00% | 14.11% | NA |
| VI/Aromatic | 96 | 78.10% | 1.00% | 0.00% | 20.83% | NA |
| Intermediate | 90 | 35.60% | 1.10% | 1.11% | 62.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0827004405 | C -> T | LOC_Os08g42700-LOC_Os08g42710 | intergenic_region ; MODIFIER | silent_mutation | Average:4.896; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0827004405 | C -> DEL | N | N | silent_mutation | Average:4.896; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0827004405 | 2.67E-06 | NA | mr1328 | 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 |
| vg0827004405 | NA | 1.95E-09 | mr1352 | 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 |
| vg0827004405 | NA | 3.14E-08 | mr1215_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 |