| Variant ID: vg1012224036 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 12224036 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GGAGCGCGAGGACGGCGGCGTGGAGCGTGAGCAGGAGGCGGCTGCGCGCAAGGCCGGCAACGGCGGTGCGGAGCGCGAGCAGGATGTGGCCGTGCGCGAG[A/G]
AGGCTGTTGAACGCTGGCCGGTACGAGGCTTGCTGCGGCCGCTGGTCGCTGGGTCTCGCCGGTATACCTACATATCCATGATCCTGGGTCTCGCAATGCA
TGCATTGCGAGACCCAGGATCATGGATATGTAGGTATACCGGCGAGACCCAGCGACCAGCGGCCGCAGCAAGCCTCGTACCGGCCAGCGTTCAACAGCCT[T/C]
CTCGCGCACGGCCACATCCTGCTCGCGCTCCGCACCGCCGTTGCCGGCCTTGCGCGCAGCCGCCTCCTGCTCACGCTCCACGCCGCCGTCCTCGCGCTCC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.60% | 0.40% | 1.38% | 49.70% | NA |
| All Indica | 2759 | 31.40% | 0.30% | 2.14% | 66.22% | NA |
| All Japonica | 1512 | 88.40% | 0.10% | 0.00% | 11.44% | NA |
| Aus | 269 | 11.90% | 2.20% | 0.37% | 85.50% | NA |
| Indica I | 595 | 11.60% | 0.50% | 3.03% | 84.87% | NA |
| Indica II | 465 | 39.60% | 0.00% | 2.58% | 57.85% | NA |
| Indica III | 913 | 34.90% | 0.30% | 1.75% | 62.98% | NA |
| Indica Intermediate | 786 | 37.40% | 0.10% | 1.65% | 60.81% | 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 | 7.30% | 0.00% | 4.17% | 88.54% | NA |
| Intermediate | 90 | 58.90% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1012224036 | A -> G | LOC_Os10g23830.1 | missense_variant ; p.Lys44Glu; MODERATE | nonsynonymous_codon ; K44E | Average:13.887; most accessible tissue: Callus, score: 51.074 | unknown | unknown | TOLERATED | 1.00 |
| vg1012224036 | A -> DEL | LOC_Os10g23830.1 | N | frameshift_variant | Average:13.887; most accessible tissue: Callus, score: 51.074 | N | N | N | N |