| Variant ID: vg1109410824 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 9410824 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
AGCTGCCTCCGCGTCTCGGCGTGCACCTTCCCGTCCTCGCCAGCCGCCGGCCACTCGCCGACGAGCCTCTCCGCCTCCCGCACCACGCCGTCGCGGCTGG[C/G]
CGCCTCGCCGTCGGCGAAGTACCACCTCCTCATCCAGCTGCCCGTGCGCGGCCTCGACTTGAGCGTCGTCAGCGTGTACCACCGGTCGGTCTTCTCCCGG
CCGGGAGAAGACCGACCGGTGGTACACGCTGACGACGCTCAAGTCGAGGCCGCGCACGGGCAGCTGGATGAGGAGGTGGTACTTCGCCGACGGCGAGGCG[G/C]
CCAGCCGCGACGGCGTGGTGCGGGAGGCGGAGAGGCTCGTCGGCGAGTGGCCGGCGGCTGGCGAGGACGGGAAGGTGCACGCCGAGACGCGGAGGCAGCT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 1.70% | 0.00% | 0.59% | NA |
| All Indica | 2759 | 99.40% | 0.00% | 0.00% | 0.58% | NA |
| All Japonica | 1512 | 98.90% | 0.70% | 0.00% | 0.46% | NA |
| Aus | 269 | 99.60% | 0.00% | 0.00% | 0.37% | NA |
| Indica I | 595 | 97.30% | 0.00% | 0.00% | 2.69% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 98.40% | 0.20% | 0.00% | 1.39% | NA |
| Japonica Intermediate | 241 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 31.20% | 68.80% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 93.30% | 2.20% | 0.00% | 4.44% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1109410824 | C -> DEL | LOC_Os11g16970.1 | N | frameshift_variant | Average:75.902; most accessible tissue: Zhenshan97 young leaf, score: 90.547 | N | N | N | N |
| vg1109410824 | C -> G | LOC_Os11g16970.1 | missense_variant ; p.Ala202Pro; MODERATE | nonsynonymous_codon ; A202P | Average:75.902; most accessible tissue: Zhenshan97 young leaf, score: 90.547 | unknown | unknown | TOLERATED | 0.07 |