| Variant ID: vg1105159978 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159978 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ATCCGGGGACGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAGGTCCATGCCTCTTCCTTACGAGCCACTCGGTCCGCGAGCTGAAAAAGCTCCGC[G/A]
GTAGTCTGGAGCTCTTTGGAGGCGATCTTTTCGATCATGCGGTTGTGCCGCACACCCCCCCTGAACGCGTAGATCACCGCGTGTGCAGGGATGCATGGTA
TACCATGCATCCCTGCACACGCGGTGATCTACGCGTTCAGGGGGGGTGTGCGGCACAACCGCATGATCGAAAAGATCGCCTCCAAAGAGCTCCAGACTAC[C/T]
GCGGAGCTTTTTCAGCTCGCGGACCGAGTGGCTCGTAAGGAAGAGGCATGGACCTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCGTCCCCGGAT
| 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 | 27.40% | 0.10% | 24.42% | 48.10% | NA |
| All Indica | 2759 | 9.40% | 0.00% | 33.71% | 56.90% | NA |
| All Japonica | 1512 | 62.90% | 0.30% | 5.42% | 31.42% | NA |
| Aus | 269 | 4.80% | 0.00% | 39.03% | 56.13% | NA |
| Indica I | 595 | 6.20% | 0.00% | 18.66% | 75.13% | NA |
| Indica II | 465 | 4.30% | 0.00% | 26.88% | 68.82% | NA |
| Indica III | 913 | 7.90% | 0.00% | 53.67% | 38.44% | NA |
| Indica Intermediate | 786 | 16.50% | 0.00% | 25.95% | 57.51% | NA |
| Temperate Japonica | 767 | 55.90% | 0.00% | 2.48% | 41.59% | NA |
| Tropical Japonica | 504 | 71.20% | 0.00% | 10.91% | 17.86% | NA |
| Japonica Intermediate | 241 | 67.60% | 1.70% | 3.32% | 27.39% | NA |
| VI/Aromatic | 96 | 38.50% | 0.00% | 25.00% | 36.46% | NA |
| Intermediate | 90 | 38.90% | 0.00% | 14.44% | 46.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159978 | G -> A | LOC_Os11g09660.1 | synonymous_variant ; p.Thr381Thr; LOW | synonymous_codon | Average:6.36; most accessible tissue: Callus, score: 13.429 | N | N | N | N |
| vg1105159978 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.36; most accessible tissue: Callus, score: 13.429 | N | N | N | N |