| Variant ID: vg1221990092 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 21990092 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
AACTCAACATGCAAGAGGAGGTGGCAAGGAAGGTTGATGAACGCATGGCCGCACATCGGTCCCATGATCCCCAGCCGACCATTCCTCCTGCAATGGTGAG[T/C]
CCGTCAGGAAACCGTAGCAGCTGCGCCTCAACGGGGCAGGTAGGATCACAGAGCATGGACGCCATGCAAACACAGGACGAATCGACCTGTCCCGTTGATG
CATCAACGGGACAGGTCGATTCGTCCTGTGTTTGCATGGCGTCCATGCTCTGTGATCCTACCTGCCCCGTTGAGGCGCAGCTGCTACGGTTTCCTGACGG[A/G]
CTCACCATTGCAGGAGGAATGGTCGGCTGGGGATCATGGGACCGATGTGCGGCCATGCGTTCATCAACCTTCCTTGCCACCTCCTCTTGCATGTTGAGTT
| 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 | 66.40% | 0.50% | 3.58% | 29.52% | NA |
| All Indica | 2759 | 54.50% | 0.00% | 3.95% | 41.50% | NA |
| All Japonica | 1512 | 91.30% | 0.00% | 0.00% | 8.66% | NA |
| Aus | 269 | 45.70% | 0.00% | 14.50% | 39.78% | NA |
| Indica I | 595 | 68.40% | 0.00% | 1.01% | 30.59% | NA |
| Indica II | 465 | 73.10% | 0.00% | 1.29% | 25.59% | NA |
| Indica III | 913 | 32.90% | 0.10% | 8.32% | 58.71% | NA |
| Indica Intermediate | 786 | 58.10% | 0.00% | 2.67% | 39.19% | NA |
| Temperate Japonica | 767 | 96.60% | 0.00% | 0.00% | 3.39% | NA |
| Tropical Japonica | 504 | 80.20% | 0.00% | 0.00% | 19.84% | NA |
| Japonica Intermediate | 241 | 97.90% | 0.00% | 0.00% | 2.07% | NA |
| VI/Aromatic | 96 | 58.30% | 22.90% | 17.71% | 1.04% | NA |
| Intermediate | 90 | 83.30% | 0.00% | 4.44% | 12.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1221990092 | T -> C | LOC_Os12g35970.1 | synonymous_variant ; p.Ser114Ser; LOW | synonymous_codon | Average:11.888; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |
| vg1221990092 | T -> DEL | LOC_Os12g35970.1 | N | frameshift_variant | Average:11.888; most accessible tissue: Minghui63 panicle, score: 25.313 | N | N | N | N |