| Variant ID: vg0204058436 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 4058436 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
TGCTCCCCGTCGAGTCGCCGGACATGATCGGCTTCGTCTCGTAGACGTCGGCGGCGAGGGAGTCCATGACGTCGATGCCGCCGTCCATCATCGGCGGCGG[C/T]
GCCATCTGCAGCTGATGATGGCCGCCGCCGCCGCACTTCCCGGCCGGGTCGTCGTCGTCGTCGTCGTCGTCGACGCCCCACATCATCGGGCTCTTCCCGG
CCGGGAAGAGCCCGATGATGTGGGGCGTCGACGACGACGACGACGACGACGACCCGGCCGGGAAGTGCGGCGGCGGCGGCCATCATCAGCTGCAGATGGC[G/A]
CCGCCGCCGATGATGGACGGCGGCATCGACGTCATGGACTCCCTCGCCGCCGACGTCTACGAGACGAAGCCGATCATGTCCGGCGACTCGACGGGGAGCA
| 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 | 96.00% | 4.00% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 97.30% | 2.60% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 58.70% | 40.50% | 0.74% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.00% | 4.90% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 97.20% | 2.70% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 4.40% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0204058436 | C -> T | LOC_Os02g07770.1 | synonymous_variant ; p.Ala280Ala; LOW | synonymous_codon | Average:62.421; most accessible tissue: Minghui63 panicle, score: 87.238 | N | N | N | N |