| Variant ID: vg0910657775 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 10657775 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
TGACCGGGAGGTCGATATGACCCAGCGGCCAGGTGTGCCCCGGCGTCACACCGATGATCGGCTGGGACGGCCGGAGCACCATCCCTGGGGCCTTGATGGC[G/A]
TCAAAGGCTGCGGGGGAAAGGATGTTGAGGGCTGCACCCCCGTCTATGAGGACACGCCCCAACTTCACATTGCAAATGGTGGGGGAAACCACCATCGCGA
TCGCGATGGTGGTTTCCCCCACCATTTGCAATGTGAAGTTGGGGCGTGTCCTCATAGACGGGGGTGCAGCCCTCAACATCCTTTCCCCCGCAGCCTTTGA[C/T]
GCCATCAAGGCCCCAGGGATGGTGCTCCGGCCGTCCCAGCCGATCATCGGTGTGACGCCGGGGCACACCTGGCCGCTGGGTCATATCGACCTCCCGGTCA
| 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 | 33.90% | 0.60% | 30.11% | 35.38% | NA |
| All Indica | 2759 | 20.90% | 1.10% | 40.92% | 37.11% | NA |
| All Japonica | 1512 | 56.50% | 0.00% | 11.44% | 32.01% | NA |
| Aus | 269 | 31.60% | 0.00% | 37.17% | 31.23% | NA |
| Indica I | 595 | 38.50% | 0.00% | 24.37% | 37.14% | NA |
| Indica II | 465 | 17.00% | 0.90% | 27.31% | 54.84% | NA |
| Indica III | 913 | 8.90% | 1.90% | 64.84% | 24.42% | NA |
| Indica Intermediate | 786 | 23.80% | 1.10% | 33.72% | 41.35% | NA |
| Temperate Japonica | 767 | 71.70% | 0.00% | 7.82% | 20.47% | NA |
| Tropical Japonica | 504 | 39.50% | 0.00% | 16.47% | 44.05% | NA |
| Japonica Intermediate | 241 | 44.00% | 0.00% | 12.45% | 43.57% | NA |
| VI/Aromatic | 96 | 52.10% | 0.00% | 5.21% | 42.71% | NA |
| Intermediate | 90 | 38.90% | 0.00% | 17.78% | 43.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910657775 | G -> DEL | LOC_Os09g17420.1 | N | frameshift_variant | Average:11.45; most accessible tissue: Callus, score: 28.743 | N | N | N | N |
| vg0910657775 | G -> A | LOC_Os09g17420.1 | synonymous_variant ; p.Asp32Asp; LOW | synonymous_codon | Average:11.45; most accessible tissue: Callus, score: 28.743 | N | N | N | N |