| Variant ID: vg0527589256 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 27589256 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATGCAGCGGTCGTCCCCTTCCTCTCGGTCGCAGGGGTCGGCGTCGGTGTTGCTCCAGGCAGCGATGCAGCGGCCATGCCCTTCCTCTCAGGTGCAGGCGC[C/T]
GGCGTTGCTCCAAGCGGCGATGCAGCCGCCGTCCTCTTCCTCGCAGGCGTCGGCGTCGGCGTTGTTCCAGGGGGCGCCCGCACGTCGACCACCGCCTCCT
AGGAGGCGGTGGTCGACGTGCGGGCGCCCCCTGGAACAACGCCGACGCCGACGCCTGCGAGGAAGAGGACGGCGGCTGCATCGCCGCTTGGAGCAACGCC[G/A]
GCGCCTGCACCTGAGAGGAAGGGCATGGCCGCTGCATCGCTGCCTGGAGCAACACCGACGCCGACCCCTGCGACCGAGAGGAAGGGGACGACCGCTGCAT
| 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 | 79.80% | 5.50% | 12.04% | 2.73% | NA |
| All Indica | 2759 | 77.70% | 1.40% | 16.78% | 4.06% | NA |
| All Japonica | 1512 | 96.80% | 0.00% | 2.38% | 0.79% | NA |
| Aus | 269 | 2.20% | 77.70% | 20.07% | 0.00% | NA |
| Indica I | 595 | 52.10% | 0.00% | 40.67% | 7.23% | NA |
| Indica II | 465 | 82.40% | 1.30% | 11.18% | 5.16% | NA |
| Indica III | 913 | 94.60% | 0.20% | 3.29% | 1.86% | NA |
| Indica Intermediate | 786 | 74.80% | 3.90% | 17.68% | 3.56% | NA |
| Temperate Japonica | 767 | 99.50% | 0.00% | 0.26% | 0.26% | NA |
| Tropical Japonica | 504 | 91.90% | 0.00% | 6.55% | 1.59% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.41% | 0.83% | NA |
| VI/Aromatic | 96 | 87.50% | 3.10% | 7.29% | 2.08% | NA |
| Intermediate | 90 | 77.80% | 8.90% | 10.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0527589256 | C -> T | LOC_Os05g48130.1 | missense_variant ; p.Pro34Leu; MODERATE | nonsynonymous_codon ; P34L | Average:28.471; most accessible tissue: Minghui63 panicle, score: 59.629 | unknown | unknown | DELETERIOUS | 0.00 |
| vg0527589256 | C -> DEL | LOC_Os05g48130.1 | N | frameshift_variant | Average:28.471; most accessible tissue: Minghui63 panicle, score: 59.629 | N | N | N | N |