| Variant ID: vg0910657733 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10657733 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
AGTCCACCCGCTCCGTGCGGAAGTTGGCGGAATCACCGATGGTGACCGGGAGGTCGATATGACCCAGCGGCCAGGTGTGCCCCGGCGTCACACCGATGAT[C/T]
GGCTGGGACGGCCGGAGCACCATCCCTGGGGCCTTGATGGCGTCAAAGGCTGCGGGGGAAAGGATGTTGAGGGCTGCACCCCCGTCTATGAGGACACGCC
GGCGTGTCCTCATAGACGGGGGTGCAGCCCTCAACATCCTTTCCCCCGCAGCCTTTGACGCCATCAAGGCCCCAGGGATGGTGCTCCGGCCGTCCCAGCC[G/A]
ATCATCGGTGTGACGCCGGGGCACACCTGGCCGCTGGGTCATATCGACCTCCCGGTCACCATCGGTGATTCCGCCAACTTCCGCACGGAGCGGGTGGACT
| 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 | 54.60% | 0.10% | 11.55% | 33.71% | NA |
| All Indica | 2759 | 49.90% | 0.00% | 15.62% | 34.51% | NA |
| All Japonica | 1512 | 63.70% | 0.50% | 5.22% | 30.62% | NA |
| Aus | 269 | 55.00% | 0.00% | 8.92% | 36.06% | NA |
| Indica I | 595 | 57.00% | 0.00% | 6.39% | 36.64% | NA |
| Indica II | 465 | 37.40% | 0.00% | 14.41% | 48.17% | NA |
| Indica III | 913 | 51.60% | 0.00% | 24.32% | 24.10% | NA |
| Indica Intermediate | 786 | 49.90% | 0.00% | 13.23% | 36.90% | NA |
| Temperate Japonica | 767 | 78.20% | 0.00% | 1.96% | 19.82% | NA |
| Tropical Japonica | 504 | 47.40% | 1.40% | 7.74% | 43.45% | NA |
| Japonica Intermediate | 241 | 51.50% | 0.00% | 10.37% | 38.17% | NA |
| VI/Aromatic | 96 | 47.90% | 0.00% | 3.12% | 48.96% | NA |
| Intermediate | 90 | 52.20% | 0.00% | 10.00% | 37.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910657733 | C -> DEL | LOC_Os09g17420.1 | N | frameshift_variant | Average:11.56; most accessible tissue: Callus, score: 28.743 | N | N | N | N |
| vg0910657733 | C -> T | LOC_Os09g17420.1 | synonymous_variant ; p.Pro46Pro; LOW | synonymous_codon | Average:11.56; most accessible tissue: Callus, score: 28.743 | N | N | N | N |