| Variant ID: vg0137498028 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 37498028 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GACCGGCGCAATCTAGGCGGGAGACGGCGTCCCAAAGCATGCCGGGCCCTACCTCGCCTGCCAAGCGGAGGGCTTCGACCTCCCCGGCGGACGAGTCCAG[C/T]
GCGCCCTGCAGATCGGCGATGGTGCGTTCGGCAGCTGCGAGGCGGGCGGCTAAGTCGCTTTCGCCCGTGGCCGCCCCGCCGCTGCGCGCCCTCGCGTCCA
TGGACGCGAGGGCGCGCAGCGGCGGGGCGGCCACGGGCGAAAGCGACTTAGCCGCCCGCCTCGCAGCTGCCGAACGCACCATCGCCGATCTGCAGGGCGC[G/A]
CTGGACTCGTCCGCCGGGGAGGTCGAAGCCCTCCGCTTGGCAGGCGAGGTAGGGCCCGGCATGCTTTGGGACGCCGTCTCCCGCCTAGATTGCGCCGGTC
| 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 | 31.70% | 0.20% | 1.27% | 66.89% | NA |
| All Indica | 2759 | 1.70% | 0.00% | 0.65% | 97.61% | NA |
| All Japonica | 1512 | 86.00% | 0.50% | 2.58% | 10.91% | NA |
| Aus | 269 | 0.40% | 0.00% | 0.00% | 99.63% | NA |
| Indica I | 595 | 0.30% | 0.00% | 1.01% | 98.66% | NA |
| Indica II | 465 | 1.10% | 0.00% | 0.22% | 98.71% | NA |
| Indica III | 913 | 0.70% | 0.00% | 0.66% | 98.69% | NA |
| Indica Intermediate | 786 | 4.50% | 0.00% | 0.64% | 94.91% | NA |
| Temperate Japonica | 767 | 84.60% | 0.00% | 2.35% | 13.04% | NA |
| Tropical Japonica | 504 | 92.90% | 1.20% | 2.38% | 3.57% | NA |
| Japonica Intermediate | 241 | 76.30% | 0.40% | 3.73% | 19.50% | NA |
| VI/Aromatic | 96 | 97.90% | 0.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 58.90% | 1.10% | 3.33% | 36.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0137498028 | C -> T | LOC_Os01g64610.1 | synonymous_variant ; p.Ala826Ala; LOW | synonymous_codon | Average:5.508; most accessible tissue: Callus, score: 15.917 | N | N | N | N |
| vg0137498028 | C -> DEL | LOC_Os01g64610.1 | N | frameshift_variant | Average:5.508; most accessible tissue: Callus, score: 15.917 | N | N | N | N |