| Variant ID: vg0521975787 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21975787 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GTTGGATCGTAGCTTCCGTGAATTTAAAACTCTGTAAATGGTAGCCAGATACTGACACATCTTGATTGTGTTATGAAGCCGTGTAGCAATGGAGGAGGAC[G/A]
TGCCGTCGCGGGTTGGATCACATGATTCAGGGCATGGAATTCCAGAGACAAGGTATGTGCATGGCTAGGTGTCAGCTGAGCATTCACTTTAAAGCAGTAT
ATACTGCTTTAAAGTGAATGCTCAGCTGACACCTAGCCATGCACATACCTTGTCTCTGGAATTCCATGCCCTGAATCATGTGATCCAACCCGCGACGGCA[C/T]
GTCCTCCTCCATTGCTACACGGCTTCATAACACAATCAAGATGTGTCAGTATCTGGCTACCATTTACAGAGTTTTAAATTCACGGAAGCTACGATCCAAC
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.30% | 1.10% | 31.89% | 20.69% | NA |
| All Indica | 2759 | 15.50% | 1.50% | 51.47% | 31.50% | NA |
| All Japonica | 1512 | 98.70% | 0.00% | 0.53% | 0.79% | NA |
| Aus | 269 | 45.00% | 4.10% | 23.05% | 27.88% | NA |
| Indica I | 595 | 16.30% | 0.00% | 44.37% | 39.33% | NA |
| Indica II | 465 | 10.50% | 4.70% | 56.13% | 28.60% | NA |
| Indica III | 913 | 18.40% | 0.50% | 51.70% | 29.35% | NA |
| Indica Intermediate | 786 | 14.50% | 1.90% | 53.82% | 29.77% | NA |
| Temperate Japonica | 767 | 98.70% | 0.00% | 0.39% | 0.91% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.20% | 0.60% | NA |
| Japonica Intermediate | 241 | 97.50% | 0.00% | 1.66% | 0.83% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 58.90% | 0.00% | 18.89% | 22.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0521975787 | G -> DEL | LOC_Os05g37540.1 | N | frameshift_variant | Average:5.468; most accessible tissue: Callus, score: 15.475 | N | N | N | N |
| vg0521975787 | G -> A | LOC_Os05g37540.1 | missense_variant ; p.Val58Met; MODERATE | nonsynonymous_codon ; V58M | Average:5.468; most accessible tissue: Callus, score: 15.475 | unknown | unknown | TOLERATED | 0.07 |