| Variant ID: vg1201734967 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 1734967 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
TGGAGCGGTGGCTGCGGGTGAGCGCCACCTGCCCGGTGTGCCGCGACTCGCCGCTGCCGTCGCCGATGGCCACGCCGCTCGCGGAGGCCGTGCCCCTCGC[T/C]
GCGCACGCTCGATGACACAGCCACACAGGTTCACATGTCACATATGTTACTGTGCTCTGTAGACAATTTTTGCTCTCTCGAATTTTCTTTGCTTCATTCG
CGAATGAAGCAAAGAAAATTCGAGAGAGCAAAAATTGTCTACAGAGCACAGTAACATATGTGACATGTGAACCTGTGTGGCTGTGTCATCGAGCGTGCGC[A/G]
GCGAGGGGCACGGCCTCCGCGAGCGGCGTGGCCATCGGCGACGGCAGCGGCGAGTCGCGGCACACCGGGCAGGTGGCGCTCACCCGCAGCCACCGCTCCA
| 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 | 44.40% | 43.00% | 6.56% | 6.07% | NA |
| All Indica | 2759 | 8.90% | 70.60% | 10.80% | 9.68% | NA |
| All Japonica | 1512 | 97.40% | 1.20% | 0.40% | 0.99% | NA |
| Aus | 269 | 83.30% | 16.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 4.90% | 73.10% | 13.61% | 8.40% | NA |
| Indica II | 465 | 6.00% | 59.80% | 12.47% | 21.72% | NA |
| Indica III | 913 | 10.00% | 77.00% | 8.87% | 4.16% | NA |
| Indica Intermediate | 786 | 12.30% | 67.80% | 9.92% | 9.92% | NA |
| Temperate Japonica | 767 | 96.00% | 1.40% | 0.65% | 1.96% | NA |
| Tropical Japonica | 504 | 98.80% | 1.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 96.90% | 3.10% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 68.90% | 21.10% | 4.44% | 5.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201734967 | T -> C | LOC_Os12g04130.1 | synonymous_variant ; p.Ala672Ala; LOW | synonymous_codon | Average:58.641; most accessible tissue: Callus, score: 97.001 | N | N | N | N |
| vg1201734967 | T -> DEL | LOC_Os12g04130.1 | N | frameshift_variant | Average:58.641; most accessible tissue: Callus, score: 97.001 | N | N | N | N |