| Variant ID: vg0908137531 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 8137531 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
ACCCGCCCATTGTCCCTGACCCAGAGTCTCCAGCCCAACGTTGGCTGGACGACGTGGCCAACTTGGTCATGACGGCACGGCAGCACCTAGGTGCTGGTGG[G/A]
CGGTCCTCCGCCACCAAGACCTCTGGCGCTGCTACCACCGGCTCCGTGTCGTCAAGGCGGAGGGCGCGGCGAGCGACGGCTATTGCTCGCCATTCGGCCG
CGGCCGAATGGCGAGCAATAGCCGTCGCTCGCCGCGCCCTCCGCCTTGACGACACGGAGCCGGTGGTAGCAGCGCCAGAGGTCTTGGTGGCGGAGGACCG[C/T]
CCACCAGCACCTAGGTGCTGCCGTGCCGTCATGACCAAGTTGGCCACGTCGTCCAGCCAACGTTGGGCTGGAGACTCTGGGTCAGGGACAATGGGCGGGT
| 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 | 38.90% | 0.10% | 5.86% | 55.14% | NA |
| All Indica | 2759 | 32.40% | 0.00% | 5.84% | 61.80% | NA |
| All Japonica | 1512 | 54.90% | 0.00% | 3.11% | 42.00% | NA |
| Aus | 269 | 7.40% | 1.50% | 11.52% | 79.55% | NA |
| Indica I | 595 | 10.40% | 0.00% | 7.56% | 82.02% | NA |
| Indica II | 465 | 63.70% | 0.00% | 2.37% | 33.98% | NA |
| Indica III | 913 | 30.10% | 0.00% | 7.34% | 62.54% | NA |
| Indica Intermediate | 786 | 33.10% | 0.00% | 4.83% | 62.09% | NA |
| Temperate Japonica | 767 | 85.10% | 0.00% | 3.13% | 11.73% | NA |
| Tropical Japonica | 504 | 21.60% | 0.00% | 1.59% | 76.79% | NA |
| Japonica Intermediate | 241 | 28.20% | 0.00% | 6.22% | 65.56% | NA |
| VI/Aromatic | 96 | 54.20% | 0.00% | 29.17% | 16.67% | NA |
| Intermediate | 90 | 48.90% | 0.00% | 11.11% | 40.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0908137531 | G -> DEL | LOC_Os09g13850.1 | N | frameshift_variant | Average:28.621; most accessible tissue: Minghui63 flag leaf, score: 61.214 | N | N | N | N |
| vg0908137531 | G -> A | LOC_Os09g13850.1 | synonymous_variant ; p.Gly124Gly; LOW | synonymous_codon | Average:28.621; most accessible tissue: Minghui63 flag leaf, score: 61.214 | N | N | N | N |