| Variant ID: vg0814381652 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 14381652 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGGCTCGCGACGAGGCCGCGGGCACATCGCCTGGGCCCACCTCCCCGGGCGACGCCCAGGATCAAACGGGTTCGGGGGACATCCCCGAGCCCAGCACGTC[C/T]
TCCGGGGGGCCGAGCCGCATCGCCTTCTCTCCAAGGCGGCTCTTCTCCTCATCTTCCGTCGCCCCGCTGAGCGCCGAGCCCATTCTGCAGGCCTTGGCCG
CGGCCAAGGCCTGCAGAATGGGCTCGGCGCTCAGCGGGGCGACGGAAGATGAGGAGAAGAGCCGCCTTGGAGAGAAGGCGATGCGGCTCGGCCCCCCGGA[G/A]
GACGTGCTGGGCTCGGGGATGTCCCCCGAACCCGTTTGATCCTGGGCGTCGCCCGGGGAGGTGGGCCCAGGCGATGTGCCCGCGGCCTCGTCGCGAGCCT
| 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 | 1.00% | 0.60% | 2.18% | 96.19% | NA |
| All Indica | 2759 | 0.50% | 1.10% | 2.46% | 95.98% | NA |
| All Japonica | 1512 | 2.10% | 0.00% | 2.25% | 95.70% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.37% | 99.26% | NA |
| Indica I | 595 | 0.80% | 0.20% | 1.51% | 97.48% | NA |
| Indica II | 465 | 0.60% | 0.20% | 0.22% | 98.92% | NA |
| Indica III | 913 | 0.40% | 2.10% | 4.16% | 93.32% | NA |
| Indica Intermediate | 786 | 0.10% | 1.10% | 2.54% | 96.18% | NA |
| Temperate Japonica | 767 | 3.50% | 0.00% | 3.39% | 93.09% | NA |
| Tropical Japonica | 504 | 0.40% | 0.00% | 0.60% | 99.01% | NA |
| Japonica Intermediate | 241 | 0.80% | 0.00% | 2.07% | 97.10% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 2.20% | 0.00% | 0.00% | 97.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0814381652 | C -> T | LOC_Os08g23760.1 | synonymous_variant ; p.Ser559Ser; LOW | synonymous_codon | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |
| vg0814381652 | C -> DEL | LOC_Os08g23760.1 | N | frameshift_variant | Average:25.733; most accessible tissue: Minghui63 panicle, score: 50.413 | N | N | N | N |