| Variant ID: vg0607895058 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7895058 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCTGGCGGACCGCGAGGCCGCCGTCACCATCCGGGAAGCAACGCTAGCGGCGCACGAGGCTGCCTGCGCCGAAGAAGAGCTCGCGCTCCGCCTCCGCGA[G/A]
GACGCGCTCACCGAGCGGGAGCGAGCTCTCGAGGGGGCCGAGGCCGCGGCGCAACAGCTGGCGGACAGCCTGTCCCTCCGCGAGGCAGCGCAGGAGGAGC
GCTCCTCCTGCGCTGCCTCGCGGAGGGACAGGCTGTCCGCCAGCTGTTGCGCCGCGGCCTCGGCCCCCTCGAGAGCTCGCTCCCGCTCGGTGAGCGCGTC[C/T]
TCGCGGAGGCGGAGCGCGAGCTCTTCTTCGGCGCAGGCAGCCTCGTGCGCCGCTAGCGTTGCTTCCCGGATGGTGACGGCGGCCTCGCGGTCCGCCAGAT
| 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 | 0.50% | 0.10% | 4.99% | 94.37% | NA |
| All Indica | 2759 | 0.00% | 0.10% | 0.07% | 99.78% | NA |
| All Japonica | 1512 | 1.70% | 0.00% | 14.29% | 84.06% | NA |
| Aus | 269 | 0.00% | 0.40% | 0.74% | 98.88% | NA |
| Indica I | 595 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Indica II | 465 | 0.00% | 0.20% | 0.00% | 99.78% | NA |
| Indica III | 913 | 0.00% | 0.30% | 0.22% | 99.45% | NA |
| Indica Intermediate | 786 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Temperate Japonica | 767 | 2.10% | 0.00% | 25.68% | 72.23% | NA |
| Tropical Japonica | 504 | 1.20% | 0.00% | 0.79% | 98.02% | NA |
| Japonica Intermediate | 241 | 1.20% | 0.00% | 6.22% | 92.53% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 10.42% | 89.58% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 6.67% | 93.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607895058 | G -> A | LOC_Os06g14150.1 | synonymous_variant ; p.Glu842Glu; LOW | synonymous_codon | Average:5.3; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg0607895058 | G -> DEL | LOC_Os06g14150.1 | N | frameshift_variant | Average:5.3; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |