| Variant ID: vg1205417079 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5417079 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TCCGTCGAGTGCCTGGACCCCGGCGTGCGCGTCCGGGCGGTCAAGTCCGGCCGCTACGAGAGCCGCATCGACGCGGAGGGCCGCGCCGCCACGGTGGACG[T/C]
CGGCGAGCTCTACGCCGACGAGGAGCGCCGCTTCCTGCTCCTCCTTGACGTGCCTCGAGCCGACGGCGACGCCGCCGTCGCCACGCGCCTCGCCAGCGTG
CACGCTGGCGAGGCGCGTGGCGACGGCGGCGTCGCCGTCGGCTCGAGGCACGTCAAGGAGGAGCAGGAAGCGGCGCTCCTCGTCGGCGTAGAGCTCGCCG[A/G]
CGTCCACCGTGGCGGCGCGGCCCTCCGCGTCGATGCGGCTCTCGTAGCGGCCGGACTTGACCGCCCGGACGCGCACGCCGGGGTCCAGGCACTCGACGGA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.40% | 0.30% | 0.99% | 61.34% | NA |
| All Indica | 2759 | 5.80% | 0.00% | 0.98% | 93.19% | NA |
| All Japonica | 1512 | 92.50% | 0.90% | 1.12% | 5.42% | NA |
| Aus | 269 | 20.40% | 0.00% | 0.74% | 78.81% | NA |
| Indica I | 595 | 6.40% | 0.00% | 2.18% | 91.43% | NA |
| Indica II | 465 | 6.50% | 0.00% | 0.86% | 92.69% | NA |
| Indica III | 913 | 3.30% | 0.00% | 0.22% | 96.50% | NA |
| Indica Intermediate | 786 | 8.00% | 0.00% | 1.02% | 90.97% | NA |
| Temperate Japonica | 767 | 92.40% | 1.70% | 2.09% | 3.78% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 0.00% | 4.96% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.40% | 0.41% | 11.62% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 1.11% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205417079 | T -> C | LOC_Os12g10250.1 | missense_variant ; p.Val332Ala; MODERATE | nonsynonymous_codon ; V332A | Average:11.046; most accessible tissue: Callus, score: 30.606 | unknown | unknown | DELETERIOUS | 0.02 |
| vg1205417079 | T -> DEL | LOC_Os12g10250.1 | N | frameshift_variant | Average:11.046; most accessible tissue: Callus, score: 30.606 | N | N | N | N |