| Variant ID: vg1105159795 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159795 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCACCTTCGCTCTTCCAAGTAGCCGAGGTCAGGGAGCGTCGGCTTCCTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCAGCGAAACGCCTTC[G/A]
ACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGCCGCCCTGTCCGAGCAGCAGATCCGGGGACGGCCGAAG
CTTCGGCCGTCCCCGGATCTGCTGCTCGGACAGGGCGGCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGT[C/T]
GAAGGCGTTTCGCTGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAGGAAGCCGACGCTCCCTGACCTCGGCTACTTGGAAGAGCGAAGGTGG
| 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 | 41.30% | 0.20% | 23.70% | 34.77% | NA |
| All Indica | 2759 | 19.00% | 0.00% | 33.24% | 47.81% | NA |
| All Japonica | 1512 | 86.20% | 0.00% | 5.16% | 8.60% | NA |
| Aus | 269 | 14.50% | 0.00% | 34.20% | 51.30% | NA |
| Indica I | 595 | 14.80% | 0.00% | 14.45% | 70.76% | NA |
| Indica II | 465 | 8.00% | 0.00% | 27.74% | 64.30% | NA |
| Indica III | 913 | 20.80% | 0.00% | 55.09% | 24.10% | NA |
| Indica Intermediate | 786 | 26.50% | 0.00% | 25.32% | 48.22% | NA |
| Temperate Japonica | 767 | 89.40% | 0.00% | 2.48% | 8.08% | NA |
| Tropical Japonica | 504 | 83.30% | 0.00% | 8.53% | 8.13% | NA |
| Japonica Intermediate | 241 | 82.20% | 0.00% | 6.64% | 11.20% | NA |
| VI/Aromatic | 96 | 43.80% | 11.50% | 25.00% | 19.79% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 10.00% | 41.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159795 | G -> A | LOC_Os11g09660.1 | synonymous_variant ; p.Val442Val; LOW | synonymous_codon | Average:5.323; most accessible tissue: Callus, score: 10.907 | N | N | N | N |
| vg1105159795 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.323; most accessible tissue: Callus, score: 10.907 | N | N | N | N |