| Variant ID: vg0128509430 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 28509430 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CTGTCAGGTGCCGTTGTACGGCGGTGCCAGATTGGGGTGTGACATATATGAACGATGGGAGGCGCGTGATGGTGGCGGTGTCTAGGCCGAACCTGGGCAG[C/T]
GTCGGCTGCTGCTGCTCCTGCTCCATGACCAGTGGACGATCACGCCGGCGACAGGCAATGCGGAGGGCTCGAGGGCAGATGAAGATGGTGATGAGGAAGA
TCTTCCTCATCACCATCTTCATCTGCCCTCGAGCCCTCCGCATTGCCTGTCGCCGGCGTGATCGTCCACTGGTCATGGAGCAGGAGCAGCAGCAGCCGAC[G/A]
CTGCCCAGGTTCGGCCTAGACACCGCCACCATCACGCGCCTCCCATCGTTCATATATGTCACACCCCAATCTGGCACCGCCGTACAACGGCACCTGACAG
| 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 | 25.10% | 9.90% | 9.65% | 55.31% | NA |
| All Indica | 2759 | 1.50% | 12.50% | 14.06% | 71.95% | NA |
| All Japonica | 1512 | 72.20% | 7.60% | 3.70% | 16.53% | NA |
| Aus | 269 | 4.50% | 0.40% | 0.74% | 94.42% | NA |
| Indica I | 595 | 1.70% | 4.50% | 7.90% | 85.88% | NA |
| Indica II | 465 | 2.60% | 9.50% | 6.24% | 81.72% | NA |
| Indica III | 913 | 0.50% | 21.40% | 28.15% | 49.95% | NA |
| Indica Intermediate | 786 | 1.90% | 9.90% | 7.00% | 81.17% | NA |
| Temperate Japonica | 767 | 92.80% | 0.00% | 0.13% | 7.04% | NA |
| Tropical Japonica | 504 | 32.90% | 21.60% | 9.92% | 35.52% | NA |
| Japonica Intermediate | 241 | 88.40% | 2.50% | 2.07% | 7.05% | NA |
| VI/Aromatic | 96 | 13.50% | 0.00% | 2.08% | 84.38% | NA |
| Intermediate | 90 | 31.10% | 11.10% | 8.89% | 48.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0128509430 | C -> T | LOC_Os01g49570.1 | synonymous_variant ; p.Thr48Thr; LOW | synonymous_codon | Average:24.383; most accessible tissue: Callus, score: 48.491 | N | N | N | N |
| vg0128509430 | C -> DEL | LOC_Os01g49570.1 | N | frameshift_variant | Average:24.383; most accessible tissue: Callus, score: 48.491 | N | N | N | N |