| Variant ID: vg0409586345 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 9586345 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GATCTTGCCGGTGCAGATCAACCCTATTCCTGCATGCAAATCGAAGAAACAAGCAAGAACAAGATAAAAGCAATCTGATATTGCAAATAGGAATTTAATA[C/T]
AAATGATAAGTTGGGGTTCCGAAGAACAAGCAGACGGACGGTCTAGCCGACACGCGCGCTGCAAGCAAGTAGCAATGGCTAAACTTTAATCTAACAAAAC
GTTTTGTTAGATTAAAGTTTAGCCATTGCTACTTGCTTGCAGCGCGCGTGTCGGCTAGACCGTCCGTCTGCTTGTTCTTCGGAACCCCAACTTATCATTT[G/A]
TATTAAATTCCTATTTGCAATATCAGATTGCTTTTATCTTGTTCTTGCTTGTTTCTTCGATTTGCATGCAGGAATAGGGTTGATCTGCACCGGCAAGATC
| 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 | 34.10% | 0.40% | 19.04% | 46.42% | NA |
| All Indica | 2759 | 19.90% | 0.60% | 17.72% | 61.76% | NA |
| All Japonica | 1512 | 66.80% | 0.00% | 14.81% | 18.39% | NA |
| Aus | 269 | 3.30% | 0.40% | 32.71% | 63.57% | NA |
| Indica I | 595 | 18.70% | 0.00% | 14.12% | 67.23% | NA |
| Indica II | 465 | 17.60% | 0.00% | 15.05% | 67.31% | NA |
| Indica III | 913 | 21.00% | 1.50% | 18.51% | 58.93% | NA |
| Indica Intermediate | 786 | 21.00% | 0.30% | 21.12% | 57.63% | NA |
| Temperate Japonica | 767 | 92.00% | 0.00% | 3.26% | 4.69% | NA |
| Tropical Japonica | 504 | 23.40% | 0.00% | 35.71% | 40.87% | NA |
| Japonica Intermediate | 241 | 77.20% | 0.00% | 7.88% | 14.94% | NA |
| VI/Aromatic | 96 | 10.40% | 2.10% | 69.79% | 17.71% | NA |
| Intermediate | 90 | 37.80% | 0.00% | 35.56% | 26.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409586345 | C -> DEL | N | N | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586345 | C -> T | LOC_Os04g17510.1 | upstream_gene_variant ; 1654.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586345 | C -> T | LOC_Os04g17530.1 | downstream_gene_variant ; 1893.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586345 | C -> T | LOC_Os04g17540.1 | downstream_gene_variant ; 4352.0bp to feature; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0409586345 | C -> T | LOC_Os04g17520.1 | intron_variant ; MODIFIER | silent_mutation | Average:4.551; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |