| Variant ID: vg1201715448 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 1715448 |
| Reference Allele: A | Alternative Allele: AT |
| Primary Allele: A | Secondary Allele: AT |
Inferred Ancestral Allele: Not determined.
AGGAATCGACCCCAACAGCGATGCCCGGAGCATCCGCGACATGCTACAAGAGTTCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTG[A/AT]
TCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGCCGACGGGGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGC
GCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCCCCGTCGGCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGA[T/AT]
CACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGAACTCTTGTAGCATGTCGCGGATGCTCCGGGCATCGCTGTTGGGGTCGATTCCT
| Populations | Population Size | Frequency of A(primary allele) | Frequency of AT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.70% | 0.30% | 0.04% | 0.00% | NA |
| All Indica | 2759 | 99.50% | 0.50% | 0.07% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 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 | 98.50% | 1.40% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715448 | A -> AT | LOC_Os12g04080.1 | upstream_gene_variant ; 784.0bp to feature; MODIFIER | N | Average:76.956; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715448 | A -> AT | LOC_Os12g04100.1 | upstream_gene_variant ; 709.0bp to feature; MODIFIER | N | Average:76.956; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715448 | A -> AT | LOC_Os12g04060.1 | downstream_gene_variant ; 4087.0bp to feature; MODIFIER | N | Average:76.956; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715448 | A -> AT | LOC_Os12g04070.1 | downstream_gene_variant ; 2671.0bp to feature; MODIFIER | N | Average:76.956; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715448 | A -> AT | LOC_Os12g04110.1 | downstream_gene_variant ; 4258.0bp to feature; MODIFIER | N | Average:76.956; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715448 | A -> AT | LOC_Os12g04090.1 | intron_variant ; MODIFIER | N | Average:76.956; most accessible tissue: Callus, score: 91.31 | N | N | N | N |