| Variant ID: vg1012224073 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224073 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
GCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAGAAGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGC[G/A]
GCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCACGGCCGCGGCGAGGATGCCCTGTCTCTATTCGCCAGC
GCTGGCGAATAGAGACAGGGCATCCTCGCCGCGGCCGTGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGC[C/T]
GCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCTTCTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGC
| 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 | 48.60% | 0.20% | 1.46% | 49.79% | NA |
| All Indica | 2759 | 31.10% | 0.20% | 2.25% | 66.40% | NA |
| All Japonica | 1512 | 88.40% | 0.10% | 0.00% | 11.44% | NA |
| Aus | 269 | 13.40% | 0.00% | 1.49% | 85.13% | NA |
| Indica I | 595 | 10.80% | 0.50% | 3.36% | 85.38% | NA |
| Indica II | 465 | 38.90% | 0.00% | 2.80% | 58.28% | NA |
| Indica III | 913 | 34.90% | 0.20% | 1.75% | 63.09% | NA |
| Indica Intermediate | 786 | 37.50% | 0.10% | 1.65% | 60.69% | NA |
| Temperate Japonica | 767 | 95.60% | 0.00% | 0.00% | 4.43% | NA |
| Tropical Japonica | 504 | 81.70% | 0.00% | 0.00% | 18.25% | NA |
| Japonica Intermediate | 241 | 79.70% | 0.80% | 0.00% | 19.50% | NA |
| VI/Aromatic | 96 | 9.40% | 0.00% | 2.08% | 88.54% | NA |
| Intermediate | 90 | 61.10% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224073 | G -> A | LOC_Os10g23830.1 | missense_variant ; p.Arg56Gln; MODERATE | nonsynonymous_codon ; R56Q | Average:14.253; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 0.23 |
| vg1012224073 | G -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:14.253; most accessible tissue: Callus, score: 51.074 | N | N | N | N |