| Variant ID: vg1012223929 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223929 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
ATCAGGGAGCAGCCGCCGCCGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGATGCGGACACGGT[C/T]
GGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTG
CACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCC[G/A]
ACCGTGTCCGCATCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCGGCGGCGGCTGCTCCCTGAT
| 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 | 50.00% | 0.00% | 0.59% | 49.41% | NA |
| All Indica | 2759 | 33.50% | 0.00% | 0.76% | 65.75% | NA |
| All Japonica | 1512 | 88.80% | 0.00% | 0.07% | 11.11% | NA |
| Aus | 269 | 11.20% | 0.40% | 2.23% | 86.25% | NA |
| Indica I | 595 | 14.80% | 0.00% | 0.67% | 84.54% | NA |
| Indica II | 465 | 41.10% | 0.00% | 1.94% | 56.99% | NA |
| Indica III | 913 | 37.10% | 0.10% | 0.33% | 62.43% | NA |
| Indica Intermediate | 786 | 38.80% | 0.00% | 0.64% | 60.56% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 81.70% | 0.00% | 0.20% | 18.06% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.00% | 18.67% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 0.00% | 90.62% | NA |
| Intermediate | 90 | 62.20% | 0.00% | 0.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223929 | C -> T | LOC_Os10g23830.1 | missense_variant ; p.Ser8Leu; MODERATE | nonsynonymous_codon ; S8L | Average:11.042; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.21 |
| vg1012223929 | C -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:11.042; most accessible tissue: Callus, score: 51.074 | N | N | N | N |