| Variant ID: vg1220959168 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 20959168 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )
TTTCACGGGGCAAACGAAGTGAACCACCTCTTTCTCCTGAGGAAGAGGCTAAGTTCGAGGCTTCGGATTGCTTGTTCCGTGGAGCATTGATCAGTGTACT[C/T]
GCTGACAACATAGTGGACGTGTACATGCACATGCCTTCTGGGAAGGACATGTGGGATGCACTTGAGGCCAAGTTCGGAGTTTCTGACGCCGGCAGTGAGC
GCTCACTGCCGGCGTCAGAAACTCCGAACTTGGCCTCAAGTGCATCCCACATGTCCTTCCCAGAAGGCATGTGCATGTACACGTCCACTATGTTGTCAGC[G/A]
AGTACACTGATCAATGCTCCACGGAACAAGCAATCCGAAGCCTCGAACTTAGCCTCTTCCTCAGGAGAAAGAGGTGGTTCACTTCGTTTGCCCCGTGAAA
| 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 | 9.90% | 0.10% | 9.82% | 80.22% | NA |
| All Indica | 2759 | 1.30% | 0.00% | 3.59% | 95.14% | NA |
| All Japonica | 1512 | 27.20% | 0.20% | 23.28% | 49.27% | NA |
| Aus | 269 | 1.50% | 0.00% | 1.12% | 97.40% | NA |
| Indica I | 595 | 1.20% | 0.00% | 3.03% | 95.80% | NA |
| Indica II | 465 | 2.60% | 0.00% | 2.15% | 95.27% | NA |
| Indica III | 913 | 0.70% | 0.00% | 5.81% | 93.54% | NA |
| Indica Intermediate | 786 | 1.30% | 0.00% | 2.29% | 96.44% | NA |
| Temperate Japonica | 767 | 39.00% | 0.00% | 39.24% | 21.77% | NA |
| Tropical Japonica | 504 | 4.40% | 0.20% | 2.98% | 92.46% | NA |
| Japonica Intermediate | 241 | 37.80% | 0.80% | 14.94% | 46.47% | NA |
| VI/Aromatic | 96 | 1.00% | 2.10% | 2.08% | 94.79% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 8.89% | 75.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1220959168 | C -> DEL | LOC_Os12g34580.1 | N | frameshift_variant | Average:14.979; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |
| vg1220959168 | C -> T | LOC_Os12g34580.1 | synonymous_variant ; p.Leu184Leu; LOW | synonymous_codon | Average:14.979; most accessible tissue: Minghui63 root, score: 29.362 | N | N | N | N |