| Variant ID: vg0233335725 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 33335725 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CAACGTAAGCGTCAAGCTCCTCTTGCGTGCAATCGTACCCCGGGTCCTTGTTCTTGGCGGCGTCAACTTTCACCTTCTTTGTTGCCCTTGTGTGGGCAAG[C/T]
GGTGGAGCTGGGGGGGCCCTTGACTTTGAAGGTGCCGGAAGAGGAGCTTGCGGGGGAGTAGGTGTAGGAGCACGAGGAGGAGTCGGTGCAGGATCCTGAG
CTCAGGATCCTGCACCGACTCCTCCTCGTGCTCCTACACCTACTCCCCCGCAAGCTCCTCTTCCGGCACCTTCAAAGTCAAGGGCCCCCCCAGCTCCACC[G/A]
CTTGCCCACACAAGGGCAACAAAGAAGGTGAAAGTTGACGCCGCCAAGAACAAGGACCCGGGGTACGATTGCACGCAAGAGGAGCTTGACGCTTACGTTG
| 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 | 36.20% | 0.10% | 0.74% | 62.89% | NA |
| All Indica | 2759 | 2.60% | 0.00% | 0.91% | 96.48% | NA |
| All Japonica | 1512 | 98.70% | 0.40% | 0.13% | 0.79% | NA |
| Aus | 269 | 2.60% | 0.00% | 2.60% | 94.80% | NA |
| Indica I | 595 | 2.20% | 0.00% | 0.84% | 96.97% | NA |
| Indica II | 465 | 3.40% | 0.00% | 1.29% | 95.27% | NA |
| Indica III | 913 | 1.20% | 0.00% | 0.99% | 97.81% | NA |
| Indica Intermediate | 786 | 4.10% | 0.00% | 0.64% | 95.29% | NA |
| Temperate Japonica | 767 | 98.20% | 0.80% | 0.26% | 0.78% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 0.00% | 2.49% | NA |
| VI/Aromatic | 96 | 89.60% | 0.00% | 1.04% | 9.38% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 0.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0233335725 | C -> T | LOC_Os02g54400.1 | synonymous_variant ; p.Pro518Pro; LOW | synonymous_codon | Average:4.532; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
| vg0233335725 | C -> DEL | LOC_Os02g54400.1 | N | frameshift_variant | Average:4.532; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |