| Variant ID: vg1012223911 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223911 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ACACCAAAAAAAAAAAATATCAGGGAGCAGCCGCCGCCGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGG[C/T]
GCGGATGCGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGC
GCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCGCATCCGC[G/A]
CCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCGGCGGCGGCTGCTCCCTGATATTTTTTTTTTTTGGTGT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 30.70% | 17.60% | 1.76% | 50.02% | NA |
| All Indica | 2759 | 2.40% | 28.30% | 2.32% | 66.94% | NA |
| All Japonica | 1512 | 88.00% | 0.40% | 0.40% | 11.18% | NA |
| Aus | 269 | 1.50% | 9.70% | 2.97% | 85.87% | NA |
| Indica I | 595 | 3.40% | 7.10% | 3.36% | 86.22% | NA |
| Indica II | 465 | 3.00% | 35.90% | 2.80% | 58.28% | NA |
| Indica III | 913 | 0.90% | 33.70% | 1.86% | 63.53% | NA |
| Indica Intermediate | 786 | 3.20% | 33.60% | 1.78% | 61.45% | NA |
| Temperate Japonica | 767 | 95.30% | 0.30% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.30% | 0.20% | 0.60% | 17.86% | NA |
| Japonica Intermediate | 241 | 78.80% | 1.20% | 1.24% | 18.67% | NA |
| VI/Aromatic | 96 | 6.20% | 3.10% | 4.17% | 86.46% | NA |
| Intermediate | 90 | 45.60% | 15.60% | 1.11% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223911 | C -> T | LOC_Os10g23830.1 | missense_variant ; p.Ala2Val; MODERATE | nonsynonymous_codon ; A2V | Average:8.866; most accessible tissue: Callus, score: 26.513 | unknown | unknown | DELETERIOUS | 0.00 |
| vg1012223911 | C -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |