| Variant ID: vg0204058642 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 4058642 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CCGTAATGCCTCGTCTTCGCCGCCGTCTTCCCCAGCGAGCCGCCGCCGTCGCCGCAGGCGAAGAAGCTCTCCATCGTCGACGCCGGCGGCTGCTGCTGCT[G/T]
CAGGTCGAGGTGGCCGCCGCCGGCGCCGCCGTACATGTGGAGGTCTTGCAGGGAAGGGAAGCCCATGGAGCACACGTCGAGCACCGCCGCCTGGTGGTTG
CAACCACCAGGCGGCGGTGCTCGACGTGTGCTCCATGGGCTTCCCTTCCCTGCAAGACCTCCACATGTACGGCGGCGCCGGCGGCGGCCACCTCGACCTG[C/A]
AGCAGCAGCAGCCGCCGGCGTCGACGATGGAGAGCTTCTTCGCCTGCGGCGACGGCGGCGGCTCGCTGGGGAAGACGGCGGCGAAGACGAGGCATTACGG
| 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 | 99.20% | 0.40% | 0.40% | 0.00% | NA |
| All Indica | 2759 | 98.60% | 0.70% | 0.69% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 96.60% | 1.00% | 2.35% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.40% | 0.30% | 0.38% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0204058642 | G -> T | LOC_Os02g07770.1 | missense_variant ; p.Gln212Lys; MODERATE | N | Average:65.472; most accessible tissue: Minghui63 panicle, score: 88.893 | N | N | N | N |