| Variant ID: vg0527589285 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 27589285 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCAGGGGTCGGCGTCGGTGTTGCTCCAGGCAGCGATGCAGCGGCCATGCCCTTCCTCTCAGGTGCAGGCGCCGGCGTTGCTCCAAGCGGCGATGCAGCCG[C/T]
CGTCCTCTTCCTCGCAGGCGTCGGCGTCGGCGTTGTTCCAGGGGGCGCCCGCACGTCGACCACCGCCTCCTCGATTTGGGGCCGACGGCCCTCTGCGCCC
GGGCGCAGAGGGCCGTCGGCCCCAAATCGAGGAGGCGGTGGTCGACGTGCGGGCGCCCCCTGGAACAACGCCGACGCCGACGCCTGCGAGGAAGAGGACG[G/A]
CGGCTGCATCGCCGCTTGGAGCAACGCCGGCGCCTGCACCTGAGAGGAAGGGCATGGCCGCTGCATCGCTGCCTGGAGCAACACCGACGCCGACCCCTGC
| 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 | 96.20% | 3.20% | 0.47% | 0.13% | NA |
| All Indica | 2759 | 94.60% | 4.30% | 0.80% | 0.22% | NA |
| All Japonica | 1512 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 92.40% | 3.70% | 3.03% | 0.84% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.43% | 0.00% | NA |
| Indica III | 913 | 95.30% | 4.60% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 92.60% | 7.10% | 0.13% | 0.13% | 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 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 72.90% | 27.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 3.30% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0527589285 | C -> T | LOC_Os05g48130.1 | missense_variant ; p.Pro44Ser; MODERATE | nonsynonymous_codon ; P44S | Average:27.481; most accessible tissue: Minghui63 panicle, score: 59.629 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0527589285 | C -> DEL | LOC_Os05g48130.1 | N | frameshift_variant | Average:27.481; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |