| Variant ID: vg1001933571 (JBrowse) | Variation Type: SNP |
| Chromosome: chr10 | Position: 1933571 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
CGCAGCTGCTATCTCCATTGATGTACAAAATAGAAGAAAAGTATGATCTGATCCGCTCATCATTGCAGACATGGCTGATCAAGGATTTCTTTCCTACCCT[G/T]
CAACCACCAATGATTGGAAGAACAAGACGAGCACCCTGGTTACCTGGATTTTGCAATAAAAAATTGATAATTTCCTGCTTCTCGACATGATGAGCAAACA
TGTTTGCTCATCATGTCGAGAAGCAGGAAATTATCAATTTTTTATTGCAAAATCCAGGTAACCAGGGTGCTCGTCTTGTTCTTCCAATCATTGGTGGTTG[C/A]
AGGGTAGGAAAGAAATCCTTGATCAGCCATGTCTGCAATGATGAGCGGATCAGATCATACTTTTCTTCTATTTTGTACATCAATGGAGATAGCAGCTGCG
| 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 | 84.20% | 0.70% | 0.34% | 14.73% | NA |
| All Indica | 2759 | 77.00% | 1.20% | 0.43% | 21.31% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 64.70% | 0.00% | 1.49% | 33.83% | NA |
| Indica I | 595 | 61.20% | 0.00% | 0.67% | 38.15% | NA |
| Indica II | 465 | 84.30% | 1.10% | 0.22% | 14.41% | NA |
| Indica III | 913 | 77.80% | 2.80% | 0.22% | 19.17% | NA |
| Indica Intermediate | 786 | 83.80% | 0.40% | 0.64% | 15.14% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 0.00% | 4.17% | NA |
| Intermediate | 90 | 93.30% | 0.00% | 0.00% | 6.67% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933571 | G -> T | LOC_Os10g04160.1 | stop_gained ; p.Cys104*; HIGH | stop_gained | Average:38.442; most accessible tissue: Callus, score: 75.859 | N | N | N | N |
| vg1001933571 | G -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:38.442; most accessible tissue: Callus, score: 75.859 | N | N | N | N |