| Variant ID: vg1012223918 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12223918 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
AAAAAAAAAATATCAGGGAGCAGCCGCCGCCGACGAGGTTGTCCACGGCAAGGGAGCGGGTAGCGGCGACCGCGCGCCAGGAGCGACCAATGGCGCGGAT[G/A]
CGGACACGGTCGGGGAGGGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGG
CCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCCCTCCCCGACCGTGTCCG[C/T]
ATCCGCGCCATTGGTCGCTCCTGGCGCGCGGTCGCCGCTACCCGCTCCCTTGCCGTGGACAACCTCGTCGGCGGCGGCTGCTCCCTGATATTTTTTTTTT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 50.00% | 0.00% | 0.76% | 49.22% | NA |
| All Indica | 2759 | 33.40% | 0.00% | 0.87% | 65.68% | NA |
| All Japonica | 1512 | 88.90% | 0.00% | 0.07% | 11.04% | NA |
| Aus | 269 | 11.50% | 0.00% | 3.35% | 85.13% | NA |
| Indica I | 595 | 14.80% | 0.00% | 0.67% | 84.54% | NA |
| Indica II | 465 | 41.90% | 0.00% | 1.08% | 56.99% | NA |
| Indica III | 913 | 36.70% | 0.10% | 0.99% | 62.21% | NA |
| Indica Intermediate | 786 | 38.70% | 0.00% | 0.76% | 60.56% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Tropical Japonica | 504 | 81.90% | 0.00% | 0.20% | 17.86% | NA |
| Japonica Intermediate | 241 | 81.30% | 0.00% | 0.00% | 18.67% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 63.30% | 0.00% | 0.00% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1012223918 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Met4Ile; MODERATE | nonsynonymous_codon ; M4R | Average:8.866; most accessible tissue: Callus, score: 26.513 | unknown | unknown | TOLERATED | 1.00 |
| vg1012223918 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:8.866; most accessible tissue: Callus, score: 26.513 | N | N | N | N |