| Variant ID: vg0221509286 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 21509286 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATGCCCGCATCAGTATCGAGCGCCGGCGTAATGGCCGACGTGCTGCCCACGCAACGGAGGGCGCCTCCTCGTCCGGAGTGTCACATCAACACGGACGCGG[G/T]
GATCAGCCCTCCGTGCCCCCGGTTGGTGGTGTCGGCTGTAGAGCCTTTGTGGCGAGCCTTCGGAACGTCCGTTGGCCCCCAAGGTTCCGGCCCACCATCG
CGATGGTGGGCCGGAACCTTGGGGGCCAACGGACGTTCCGAAGGCTCGCCACAAAGGCTCTACAGCCGACACCACCAACCGGGGGCACGGAGGGCTGATC[C/A]
CCGCGTCCGTGTTGATGTGACACTCCGGACGAGGAGGCGCCCTCCGTTGCGTGGGCAGCACGTCGGCCATTACGCCGGCGCTCGATACTGATGCGGGCAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.90% | 0.10% | 2.31% | 62.70% | NA |
| All Indica | 2759 | 2.90% | 0.00% | 2.68% | 94.45% | NA |
| All Japonica | 1512 | 94.40% | 0.20% | 2.12% | 3.24% | NA |
| Aus | 269 | 1.10% | 0.00% | 0.37% | 98.51% | NA |
| Indica I | 595 | 2.90% | 0.00% | 1.85% | 95.29% | NA |
| Indica II | 465 | 3.00% | 0.00% | 3.66% | 93.33% | NA |
| Indica III | 913 | 2.20% | 0.00% | 2.08% | 95.73% | NA |
| Indica Intermediate | 786 | 3.60% | 0.00% | 3.44% | 93.00% | NA |
| Temperate Japonica | 767 | 94.70% | 0.40% | 3.78% | 1.17% | NA |
| Tropical Japonica | 504 | 93.10% | 0.00% | 0.40% | 6.55% | NA |
| Japonica Intermediate | 241 | 96.70% | 0.00% | 0.41% | 2.90% | NA |
| VI/Aromatic | 96 | 91.70% | 0.00% | 1.04% | 7.29% | NA |
| Intermediate | 90 | 56.70% | 2.20% | 1.11% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0221509286 | G -> T | LOC_Os02g35800.1 | synonymous_variant ; p.Gly208Gly; LOW | synonymous_codon | Average:5.563; most accessible tissue: Callus, score: 14.511 | N | N | N | N |
| vg0221509286 | G -> DEL | LOC_Os02g35800.1 | N | frameshift_variant | Average:5.563; most accessible tissue: Callus, score: 14.511 | N | N | N | N |