| Variant ID: vg1218480729 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18480729 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTCTGTTCTGAATGATGAGCCAAGCATGAAATTTGCATTTCCCCGGCGCCCAGGGTTTCCAAATCAAGGAATTGAAGTTTGTACTCGGCGCCCCGCAGCA[C/T]
TGCGCATGGTAAGCCGAGGAGGCCGTGTAGTGCCCGTTGTTTGTGAACTTCCAAGTAATCTGATCCGGTTCTCCAACATCTAAGTGCACATTTCGGACCG
CGGTCCGAAATGTGCACTTAGATGTTGGAGAACCGGATCAGATTACTTGGAAGTTCACAAACAACGGGCACTACACGGCCTCCTCGGCTTACCATGCGCA[G/A]
TGCTGCGGGGCGCCGAGTACAAACTTCAATTCCTTGATTTGGAAACCCTGGGCGCCGGGGAAATGCAAATTTCATGCTTGGCTCATCATTCAGAACAGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.80% | 0.40% | 12.63% | 49.24% | NA |
| All Indica | 2759 | 33.00% | 0.60% | 16.71% | 49.69% | NA |
| All Japonica | 1512 | 39.00% | 0.00% | 3.31% | 57.67% | NA |
| Aus | 269 | 71.40% | 0.40% | 18.59% | 9.67% | NA |
| Indica I | 595 | 16.60% | 0.50% | 17.98% | 64.87% | NA |
| Indica II | 465 | 27.50% | 0.20% | 15.91% | 56.34% | NA |
| Indica III | 913 | 47.20% | 0.90% | 17.20% | 34.72% | NA |
| Indica Intermediate | 786 | 32.20% | 0.50% | 15.65% | 51.65% | NA |
| Temperate Japonica | 767 | 60.80% | 0.00% | 1.43% | 37.81% | NA |
| Tropical Japonica | 504 | 10.90% | 0.00% | 6.35% | 82.74% | NA |
| Japonica Intermediate | 241 | 28.60% | 0.00% | 2.90% | 68.46% | NA |
| VI/Aromatic | 96 | 46.90% | 0.00% | 25.00% | 28.12% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 13.33% | 34.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480729 | C -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:6.845; most accessible tissue: Callus, score: 17.876 | N | N | N | N |
| vg1218480729 | C -> T | LOC_Os12g30780.1 | synonymous_variant ; p.Gln94Gln; LOW | synonymous_codon | Average:6.845; most accessible tissue: Callus, score: 17.876 | N | N | N | N |