| Variant ID: vg1001933542 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr10 | Position: 1933542 |
| Reference Allele: T | Alternative Allele: TGGCTGAA |
| Primary Allele: T | Secondary Allele: TGGCTGAA |
Inferred Ancestral Allele: Not determined.
CATTTTGAACTTTGCATGTGCTATTGATCCGCAGCTGCTATCTCCATTGATGTACAAAATAGAAGAAAAGTATGATCTGATCCGCTCATCATTGCAGACA[T/TGGCTGAA]
GGCTGATCAAGGATTTCTTTCCTACCCTGCAACCACCAATGATTGGAAGAACAAGACGAGCACCCTGGTTACCTGGATTTTGCAATAAAAAATTGATAAT
ATTATCAATTTTTTATTGCAAAATCCAGGTAACCAGGGTGCTCGTCTTGTTCTTCCAATCATTGGTGGTTGCAGGGTAGGAAAGAAATCCTTGATCAGCC[A/TTCAGCCA]
TGTCTGCAATGATGAGCGGATCAGATCATACTTTTCTTCTATTTTGTACATCAATGGAGATAGCAGCTGCGGATCAATAGCACATGCAAAGTTCAAAATG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TGGCTGAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 84.10% | 0.70% | 0.49% | 14.77% | NA |
| All Indica | 2759 | 76.80% | 1.10% | 0.76% | 21.31% | NA |
| All Japonica | 1512 | 99.50% | 0.00% | 0.00% | 0.46% | NA |
| Aus | 269 | 64.70% | 0.00% | 0.74% | 34.57% | NA |
| Indica I | 595 | 60.50% | 0.00% | 1.18% | 38.32% | NA |
| Indica II | 465 | 85.20% | 0.00% | 0.22% | 14.62% | NA |
| Indica III | 913 | 77.90% | 2.80% | 0.33% | 18.95% | NA |
| Indica Intermediate | 786 | 83.00% | 0.60% | 1.27% | 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 | 92.20% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1001933542 | T -> TGGCTGAA | LOC_Os10g04160.1 | frameshift_variant ; p.His114fs; HIGH | frameshift_variant | Average:38.982; most accessible tissue: Callus, score: 75.859 | N | N | N | N |
| vg1001933542 | T -> DEL | LOC_Os10g04160.1 | N | frameshift_variant | Average:38.982; most accessible tissue: Callus, score: 75.859 | N | N | N | N |