| Variant ID: vg0620603108 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 20603108 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGGATCATATTCTAGAAAATACTTCCTTCATGACGCAATCTGATGAACCCCAACCGGAGGCATACGTGTCCAAAATAGAGGAACCTCTAACGATCGAGCC[G/A]
CTCACTGAACCATCCACTTCTGCTAGCTCGATTGATGAGAAGGTTGCTAAGCAGCCGTCCGTCGAGAATGAAGAAATTCAGACTCCGGATCGTGCCGCAA
TTGCGGCACGATCCGGAGTCTGAATTTCTTCATTCTCGACGGACGGCTGCTTAGCAACCTTCTCATCAATCGAGCTAGCAGAAGTGGATGGTTCAGTGAG[C/T]
GGCTCGATCGTTAGAGGTTCCTCTATTTTGGACACGTATGCCTCCGGTTGGGGTTCATCAGATTGCGTCATGAAGGAAGTATTTTCTAGAATATGATCCA
| 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 | 97.60% | 0.90% | 0.25% | 1.23% | NA |
| All Indica | 2759 | 98.00% | 1.60% | 0.40% | 0.07% | NA |
| All Japonica | 1512 | 96.40% | 0.00% | 0.07% | 3.57% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.00% | 0.17% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.00% | 0.22% | 0.00% | NA |
| Indica III | 913 | 94.20% | 4.70% | 0.99% | 0.11% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.00% | 0.13% | NA |
| Temperate Japonica | 767 | 99.20% | 0.00% | 0.00% | 0.78% | NA |
| Tropical Japonica | 504 | 98.60% | 0.00% | 0.20% | 1.19% | NA |
| Japonica Intermediate | 241 | 82.60% | 0.00% | 0.00% | 17.43% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 1.10% | 0.00% | 2.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0620603108 | G -> A | LOC_Os06g35340.1 | synonymous_variant ; p.Pro184Pro; LOW | synonymous_codon | Average:5.749; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |
| vg0620603108 | G -> DEL | LOC_Os06g35340.1 | N | frameshift_variant | Average:5.749; most accessible tissue: Zhenshan97 root, score: 10.511 | N | N | N | N |