| Variant ID: vg0430654071 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 30654071 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GGACCAGATCAACTGCATCATTGAGAGCTGTCGGCCAATAGAACCCTTGACGAAAGGCCTTGCCAACCAAGGTGCGCGAGGCGGAATGGGCTCCGCACTC[G/A]
CCTTCATGGATATCGGCAAGAAGCTCAACGCCTTGTTCCTGAGGAATGCACTTCAGGAGGATTCCGTTAGCCGCGCGCCGATAGAGGGTCCCTTCTATCA
TGATAGAAGGGACCCTCTATCGGCGCGCGGCTAACGGAATCCTCCTGAAGTGCATTCCTCAGGAACAAGGCGTTGAGCTTCTTGCCGATATCCATGAAGG[C/T]
GAGTGCGGAGCCCATTCCGCCTCGCGCACCTTGGTTGGCAAGGCCTTTCGTCAAGGGTTCTATTGGCCGACAGCTCTCAATGATGCAGTTGATCTGGTCC
| 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 | 84.10% | 0.40% | 0.40% | 15.09% | NA |
| All Indica | 2759 | 98.70% | 0.40% | 0.18% | 0.69% | NA |
| All Japonica | 1512 | 56.40% | 0.00% | 0.79% | 42.79% | NA |
| Aus | 269 | 90.00% | 1.50% | 0.74% | 7.81% | NA |
| Indica I | 595 | 99.30% | 0.00% | 0.50% | 0.17% | NA |
| Indica II | 465 | 99.40% | 0.00% | 0.00% | 0.65% | NA |
| Indica III | 913 | 98.50% | 1.20% | 0.22% | 0.11% | NA |
| Indica Intermediate | 786 | 98.10% | 0.10% | 0.00% | 1.78% | NA |
| Temperate Japonica | 767 | 65.60% | 0.00% | 0.39% | 34.03% | NA |
| Tropical Japonica | 504 | 46.20% | 0.00% | 0.99% | 52.78% | NA |
| Japonica Intermediate | 241 | 48.50% | 0.00% | 1.66% | 49.79% | NA |
| VI/Aromatic | 96 | 80.20% | 1.00% | 0.00% | 18.75% | NA |
| Intermediate | 90 | 90.00% | 1.10% | 0.00% | 8.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0430654071 | G -> DEL | LOC_Os04g51730.1 | N | frameshift_variant | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |
| vg0430654071 | G -> A | LOC_Os04g51730.1 | synonymous_variant ; p.Gly97Gly; LOW | synonymous_codon | Average:9.174; most accessible tissue: Zhenshan97 flag leaf, score: 14.661 | N | N | N | N |