| Variant ID: vg0910529819 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr09 | Position: 10529819 |
| Reference Allele: TC | Alternative Allele: T |
| Primary Allele: TC | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
GCTTCCCGCCATTGAATCATCGTGGTTTTCTAAGGATGTCCACCTTCCCTCCTCTCGGGAAGTGGCTCCATCAGCATAAAATTCATCATGCAATATCCCA[TC/T]
CCCCACAAGTTAAGAATTTAGAGTGTAGCCAAGTGTAATACATGTCCCGGTGCTCAATAACCGCGAGCACGGCTATTCGAATAGATTTGGTTTACTCACA
TGTGAGTAAACCAAATCTATTCGAATAGCCGTGCTCGCGGTTATTGAGCACCGGGACATGTATTACACTTGGCTACACTCTAAATTCTTAACTTGTGGGG[GA/A]
TGGGATATTGCATGATGAATTTTATGCTGATGGAGCCACTTCCCGAGAGGAGGGAAGGTGGACATCCTTAGAAAACCACGATGATTCAATGGCGGGAAGC
| Populations | Population Size | Frequency of TC(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 76.00% | 0.10% | 2.07% | 21.79% | NA |
| All Indica | 2759 | 88.40% | 0.10% | 2.21% | 9.31% | NA |
| All Japonica | 1512 | 50.00% | 0.00% | 2.18% | 47.82% | NA |
| Aus | 269 | 95.90% | 1.10% | 0.74% | 2.23% | NA |
| Indica I | 595 | 91.10% | 0.00% | 2.86% | 6.05% | NA |
| Indica II | 465 | 81.30% | 0.00% | 1.08% | 17.63% | NA |
| Indica III | 913 | 91.00% | 0.00% | 1.20% | 7.78% | NA |
| Indica Intermediate | 786 | 87.50% | 0.30% | 3.56% | 8.65% | NA |
| Temperate Japonica | 767 | 52.90% | 0.00% | 2.22% | 44.85% | NA |
| Tropical Japonica | 504 | 54.40% | 0.00% | 1.19% | 44.44% | NA |
| Japonica Intermediate | 241 | 31.50% | 0.00% | 4.15% | 64.32% | NA |
| VI/Aromatic | 96 | 79.20% | 0.00% | 2.08% | 18.75% | NA |
| Intermediate | 90 | 71.10% | 0.00% | 0.00% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0910529819 | TC -> DEL | N | N | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |
| vg0910529819 | TC -> T | LOC_Os09g17160.1 | intron_variant ; MODIFIER | silent_mutation | Average:10.82; most accessible tissue: Callus, score: 36.782 | N | N | N | N |