| Variant ID: vg0607893794 (JBrowse) | Variation Type: SNP |
| Chromosome: chr06 | Position: 7893794 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TCGCAGGTTCGTCTCTCACCCATCGTGGCTGTATTCATTCTCTCAACGCGAGTTTTCACTCACCCATCTTGTTCGTCTTCTGGTCTTTTCTTTTGTTTCA[G/A]
CGAGATCCCGTCGCGTCCCTCCCGCCATTCCAAGTCCGGCCAGTCTGAGGCCGAGGATCCGGCGACCGCAGAGGCCCGCAGGCGGCAAGCTGACCGGCGA
TCGCCGGTCAGCTTGCCGCCTGCGGGCCTCTGCGGTCGCCGGATCCTCGGCCTCAGACTGGCCGGACTTGGAATGGCGGGAGGGACGCGACGGGATCTCG[C/T]
TGAAACAAAAGAAAAGACCAGAAGACGAACAAGATGGGTGAGTGAAAACTCGCGTTGAGAGAATGAATACAGCCACGATGGGTGAGAGACGAACCTGCGA
| 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 | 8.30% | 0.10% | 2.43% | 89.17% | NA |
| All Indica | 2759 | 2.70% | 0.20% | 3.66% | 93.44% | NA |
| All Japonica | 1512 | 19.90% | 0.00% | 0.60% | 79.50% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.74% | 97.77% | NA |
| Indica I | 595 | 1.30% | 0.00% | 1.68% | 96.97% | NA |
| Indica II | 465 | 1.10% | 0.00% | 2.58% | 96.34% | NA |
| Indica III | 913 | 5.40% | 0.70% | 5.81% | 88.17% | NA |
| Indica Intermediate | 786 | 1.50% | 0.00% | 3.31% | 95.17% | NA |
| Temperate Japonica | 767 | 33.80% | 0.00% | 0.00% | 66.23% | NA |
| Tropical Japonica | 504 | 3.80% | 0.00% | 1.59% | 94.64% | NA |
| Japonica Intermediate | 241 | 9.50% | 0.00% | 0.41% | 90.04% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 1.04% | 96.88% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 2.22% | 86.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0607893794 | G -> A | LOC_Os06g14150.1 | splice_acceptor_variant&intron_variant ; HIGH | splice_acceptor_variant | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |
| vg0607893794 | G -> DEL | LOC_Os06g14150.1 | N | splice_acceptor_variant | Average:6.831; most accessible tissue: Callus, score: 21.877 | N | N | N | N |