| Variant ID: vg0300827025 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 827025 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
ATTTTGACGGGATTGAGCTTCGGCATGTGCCCAGACGGGATAACATGATTGCCGACGAACTCTCACGGCTCGCGTCCTCGCGAGCCCAGACCCCACCGGG[T/C]
GCCTTTGAAGAAAGGCTTACCCAGCCGTCGGCGCGACCCGACCCCTTAGGGGAGACGGATGCGCCTGACCGGCCCCCGAGGCCCGTCGGAGTCCAGGCCT
AGGCCTGGACTCCGACGGGCCTCGGGGGCCGGTCAGGCGCATCCGTCTCCCCTAAGGGGTCGGGTCGCGCCGACGGCTGGGTAAGCCTTTCTTCAAAGGC[A/G]
CCCGGTGGGGTCTGGGCTCGCGAGGACGCGAGCCGTGAGAGTTCGTCGGCAATCATGTTATCCCGTCTGGGCACATGCCGAAGCTCAATCCCGTCAAAAT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.00% | 1.60% | 2.20% | 84.17% | NA |
| All Indica | 2759 | 2.20% | 0.10% | 2.72% | 95.00% | NA |
| All Japonica | 1512 | 32.10% | 4.80% | 1.46% | 61.57% | NA |
| Aus | 269 | 0.00% | 0.70% | 0.74% | 98.51% | NA |
| Indica I | 595 | 0.20% | 0.00% | 1.51% | 98.32% | NA |
| Indica II | 465 | 6.20% | 0.00% | 3.66% | 90.11% | NA |
| Indica III | 913 | 1.90% | 0.20% | 2.52% | 95.40% | NA |
| Indica Intermediate | 786 | 1.80% | 0.00% | 3.31% | 94.91% | NA |
| Temperate Japonica | 767 | 55.00% | 5.00% | 1.43% | 38.59% | NA |
| Tropical Japonica | 504 | 6.20% | 0.40% | 1.59% | 91.87% | NA |
| Japonica Intermediate | 241 | 13.70% | 13.70% | 1.24% | 71.37% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 3.12% | 92.71% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 2.22% | 80.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0300827025 | T -> C | LOC_Os03g02350.1 | synonymous_variant ; p.Gly1568Gly; LOW | synonymous_codon | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0300827025 | T -> DEL | LOC_Os03g02350.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |