| Variant ID: vg1218480220 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480220 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACTAGAGTGCCTTTTCATCGAATAGAGCAGGAGAAAATACAAACCCCTAGGGGTAAAAGAAAAACGGAGAACCACTATAGCTGTACACTATACAGAGTGT[G/A]
GGATTAACTCACGCAACCGCTTAGCTCCTGCTAAAGCCCAAAGGCTCGCCTCCTCTTTGATTTTCATTAGTAGGAAGTTCGTTGCCACCTCTTTGTGATC
GATCACAAAGAGGTGGCAACGAACTTCCTACTAATGAAAATCAAAGAGGAGGCGAGCCTTTGGGCTTTAGCAGGAGCTAAGCGGTTGCGTGAGTTAATCC[C/T]
ACACTCTGTATAGTGTACAGCTATAGTGGTTCTCCGTTTTTCTTTTACCCCTAGGGGTTTGTATTTTCTCCTGCTCTATTCGATGAAAAGGCACTCTAGT
| 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 | 16.80% | 1.80% | 8.97% | 72.45% | NA |
| All Indica | 2759 | 6.10% | 0.90% | 9.68% | 83.33% | NA |
| All Japonica | 1512 | 35.30% | 1.20% | 1.12% | 62.43% | NA |
| Aus | 269 | 22.70% | 8.90% | 41.64% | 26.77% | NA |
| Indica I | 595 | 5.50% | 0.00% | 4.54% | 89.92% | NA |
| Indica II | 465 | 3.90% | 1.10% | 6.02% | 89.03% | NA |
| Indica III | 913 | 6.10% | 1.00% | 15.77% | 77.11% | NA |
| Indica Intermediate | 786 | 7.80% | 1.40% | 8.65% | 82.19% | NA |
| Temperate Japonica | 767 | 60.00% | 0.00% | 0.39% | 39.63% | NA |
| Tropical Japonica | 504 | 3.20% | 3.40% | 2.18% | 91.27% | NA |
| Japonica Intermediate | 241 | 23.70% | 0.40% | 1.24% | 74.69% | NA |
| VI/Aromatic | 96 | 1.00% | 15.60% | 18.75% | 64.58% | NA |
| Intermediate | 90 | 33.30% | 3.30% | 11.11% | 52.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480220 | G -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:10.282; most accessible tissue: Callus, score: 21.903 | N | N | N | N |
| vg1218480220 | G -> A | LOC_Os12g30780.1 | missense_variant ; p.Pro264Leu; MODERATE | nonsynonymous_codon ; P264L | Average:10.282; most accessible tissue: Callus, score: 21.903 | unknown | unknown | TOLERATED | 0.05 |