| Variant ID: vg0128509406 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509406 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCCGTTTTTCCCACGACACGCTCCTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGC[G/T]
GTGTCTAGGCCGAACCTGGGCAGCGTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGC
GCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGACGCTGCCCAGGTTCGGCCTAGACAC[C/A]
GCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAGGAGCGTGTCGTGGGAAAAACGGCG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 49.60% | 0.30% | 6.90% | 43.27% | NA |
| All Indica | 2759 | 33.50% | 0.00% | 10.47% | 56.00% | NA |
| All Japonica | 1512 | 88.90% | 0.80% | 0.66% | 9.66% | NA |
| Aus | 269 | 2.20% | 0.00% | 8.18% | 89.59% | NA |
| Indica I | 595 | 17.00% | 0.00% | 8.40% | 74.62% | NA |
| Indica II | 465 | 28.80% | 0.00% | 9.46% | 61.72% | NA |
| Indica III | 913 | 51.50% | 0.00% | 13.14% | 35.38% | NA |
| Indica Intermediate | 786 | 28.00% | 0.00% | 9.54% | 62.47% | NA |
| Temperate Japonica | 767 | 92.70% | 0.00% | 0.39% | 6.91% | NA |
| Tropical Japonica | 504 | 79.60% | 2.20% | 1.19% | 17.06% | NA |
| Japonica Intermediate | 241 | 96.30% | 0.40% | 0.41% | 2.90% | NA |
| VI/Aromatic | 96 | 18.80% | 0.00% | 3.12% | 78.12% | NA |
| Intermediate | 90 | 55.60% | 0.00% | 2.22% | 42.22% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509406 | G -> T | LOC_Os01g49570.1 | synonymous_variant ; p.Thr56Thr; LOW | synonymous_codon | Average:21.721; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |
| vg0128509406 | G -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:21.721; most accessible tissue: Zhenshan97 panicle, score: 39.652 | N | N | N | N |