| Variant ID: vg1212722844 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 12722844 |
| Reference Allele: AC | Alternative Allele: A |
| Primary Allele: AC | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
CCTCTGGTTATATTTATAGAGGGGGTGATTATGATCCAGGAATGGTGCACTATGGTGAGTTGTGTTGTGCAGGGGGTACTGTCACAGCCTCTATTCGGGT[AC/A]
TTTCCAGTATCGCGACGCATGGTAGACATGATGTTGAGGCTGTGTCTTGTGTGTACAGTGGTACACCTCTGGCCAGAGTAAAACTATTCGAATAGCCGTG
CACGGCTATTCGAATAGTTTTACTCTGGCCAGAGGTGTACCACTGTACACACAAGACACAGCCTCAACATCATGTCTACCATGCGTCGCGATACTGGAAA[GT/T]
ACCCGAATAGAGGCTGTGACAGTACCCCCTGCACAACACAACTCACCATAGTGCACCATTCCTGGATCATAATCACCCCCTCTATAAATATAACCAGAGG
| Populations | Population Size | Frequency of AC(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 97.60% | 2.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1212722844 | AC -> A | LOC_Os12g22530.1 | downstream_gene_variant ; 4391.0bp to feature; MODIFIER | N | Average:55.301; most accessible tissue: Zhenshan97 flag leaf, score: 76.642 | N | N | N | N |
| vg1212722844 | AC -> A | LOC_Os12g22540.1 | intron_variant ; MODIFIER | N | Average:55.301; most accessible tissue: Zhenshan97 flag leaf, score: 76.642 | N | N | N | N |