| Variant ID: vg1218481413 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 18481413 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
TTCCCTCGGCTCCGCAAAGTCGAGCTCTACCCCGGCCACCCGTTCTTTTGCGCTGAACCCCGCCGGAAGTCGCCGTCACCGTGAAGGCCGAACCGTTGCC[A/G]
TGTTTTGATCTCCAACGAAGCTTTGCCGTCGACTCCGTGGTCGCCGGACCTCGCCGTATCCACTGTCGGCATCGCAGCAGTGAGGAGAAGCCTGGCAGCC
GGCTGCCAGGCTTCTCCTCACTGCTGCGATGCCGACAGTGGATACGGCGAGGTCCGGCGACCACGGAGTCGACGGCAAAGCTTCGTTGGAGATCAAAACA[T/C]
GGCAACGGTTCGGCCTTCACGGTGACGGCGACTTCCGGCGGGGTTCAGCGCAAAAGAACGGGTGGCCGGGGTAGAGCTCGACTTTGCGGAGCCGAGGGAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 13.10% | 0.30% | 2.14% | 84.49% | NA |
| All Indica | 2759 | 2.10% | 0.50% | 2.43% | 95.00% | NA |
| All Japonica | 1512 | 35.10% | 0.00% | 0.40% | 64.48% | NA |
| Aus | 269 | 1.50% | 0.00% | 9.29% | 89.22% | NA |
| Indica I | 595 | 3.40% | 0.00% | 0.50% | 96.13% | NA |
| Indica II | 465 | 2.80% | 0.00% | 2.58% | 94.62% | NA |
| Indica III | 913 | 0.30% | 1.40% | 3.07% | 95.18% | NA |
| Indica Intermediate | 786 | 2.80% | 0.00% | 3.05% | 94.15% | NA |
| Temperate Japonica | 767 | 59.70% | 0.00% | 0.26% | 40.03% | NA |
| Tropical Japonica | 504 | 3.00% | 0.00% | 0.60% | 96.43% | NA |
| Japonica Intermediate | 241 | 24.10% | 0.00% | 0.41% | 75.52% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 27.80% | 1.10% | 3.33% | 67.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1218481413 | A -> DEL | LOC_Os12g30780.1 | N | frameshift_variant | Average:22.104; most accessible tissue: Minghui63 young leaf, score: 39.381 | N | N | N | N |
| vg1218481413 | A -> G | LOC_Os12g30780.1 | missense_variant ; p.Trp42Arg; MODERATE | nonsynonymous_codon ; W42R | Average:22.104; most accessible tissue: Minghui63 young leaf, score: 39.381 | unknown | unknown | TOLERATED | 0.17 |