| Variant ID: vg1205416356 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 5416356 |
| Reference Allele: G | Alternative Allele: C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CGCTCTCGCGCGGCGCCGCGCGCGACGGCTTCGCCGTGCTGGTGCACGCCAAGGCGCCCGCGGCGGCGGCCGAGGCGGCGGGGCGCGCGCCGCTGGACCT[G/C]
GTCACGGTGCTCGACGTCAGCACGAGCATGACCGGGGACAAGCTGGCGCTGGTGAAGCGCGCCATGGGGTTCGTCATCGACAGCCTCGGCGCCGCCGACC
GGTCGGCGGCGCCGAGGCTGTCGATGACGAACCCCATGGCGCGCTTCACCAGCGCCAGCTTGTCCCCGGTCATGCTCGTGCTGACGTCGAGCACCGTGAC[C/G]
AGGTCCAGCGGCGCGCGCCCCGCCGCCTCGGCCGCCGCCGCGGGCGCCTTGGCGTGCACCAGCACGGCGAAGCCGTCGCGCGCGGCGCCGCGCGAGAGCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 37.60% | 0.10% | 0.34% | 61.96% | NA |
| All Indica | 2759 | 5.30% | 0.10% | 0.51% | 94.09% | NA |
| All Japonica | 1512 | 94.40% | 0.00% | 0.00% | 5.62% | NA |
| Aus | 269 | 19.70% | 0.40% | 0.74% | 79.18% | NA |
| Indica I | 595 | 5.90% | 0.00% | 0.34% | 93.78% | NA |
| Indica II | 465 | 4.90% | 0.00% | 0.43% | 94.62% | NA |
| Indica III | 913 | 3.20% | 0.20% | 0.33% | 96.28% | NA |
| Indica Intermediate | 786 | 7.40% | 0.30% | 0.89% | 91.48% | NA |
| Temperate Japonica | 767 | 96.10% | 0.00% | 0.00% | 3.91% | NA |
| Tropical Japonica | 504 | 95.00% | 0.00% | 0.00% | 4.96% | NA |
| Japonica Intermediate | 241 | 87.60% | 0.00% | 0.00% | 12.45% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 70.00% | 0.00% | 0.00% | 30.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1205416356 | G -> C | LOC_Os12g10250.1 | synonymous_variant ; p.Leu132Leu; LOW | synonymous_codon | Average:17.653; most accessible tissue: Callus, score: 50.768 | N | N | N | N |
| vg1205416356 | G -> DEL | LOC_Os12g10250.1 | N | frameshift_variant | Average:17.653; most accessible tissue: Callus, score: 50.768 | N | N | N | N |