| Variant ID: vg1123252936 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 23252936 |
| Reference Allele: ATCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACC | Alternative Allele: GTCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACC,A |
| Primary Allele: ATCGGCGAGGTAGCTCTCGC CGACGACGTAGCAGCCGTTG TCCTCGACCTGGCGGCTGAC C | Secondary Allele: GTCGGCGAGGTAGCTCTCGC CGACGACGTAGCAGCCGTTG TCCTCGACCTGGCGGCTGAC C |
Inferred Ancestral Allele: Not determined.
TGTCCACACACATCTCAATATCTCATGGCTACTCGAATTCGAAGGCGCTCCAGTCGATCTTGGCCCATTCTTCGTTGATCAGAGCCTCGAGCTTGGCCTG[ATCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACC/GTCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACC,A]
TCGGCCTGGAACACGGCGAGGTCGTCGTCCAAAGCCTTGTGCAGGGCGGCCATCTTGTCGATCTCCCGGCGCTGCTCCGGCGAGAGGTGCTTCAGGTCGT
ACGACCTGAAGCACCTCTCGCCGGAGCAGCGCCGGGAGATCGACAAGATGGCCGCCCTGCACAAGGCTTTGGACGACGACCTCGCCGTGTTCCAGGCCGA[GGTCAGCCGCCAGGTCGAGGACAACGGCTGCTACGTCGTCGGCGAGAGCTACCTCGCCGAT/GGTCAGCCGCCAGGTCGAGGACAACGGCTGCTACGTCGTCGGCGAGAGCTACCTCGCCGAC,T]
CAGGCCAAGCTCGAGGCTCTGATCAACGAAGAATGGGCCAAGATCGACTGGAGCGCCTTCGAATTCGAGTAGCCATGAGATATTGAGATGTGTGTGGACA
| Populations | Population Size | Frequency of ATCGGCGAGGTAGCTCTCGC CGACGACGTAGCAGCCGTTG TCCTCGACCTGGCGGCTGAC C(primary allele) | Frequency of GTCGGCGAGGTAGCTCTCGC CGACGACGTAGCAGCCGTTG TCCTCGACCTGGCGGCTGAC C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.40% | 0.02% | 0.00% | A: 0.02% |
| All Indica | 2759 | 99.70% | 0.20% | 0.04% | 0.00% | A: 0.04% |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.50% | 4.50% | 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 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.10% | 0.13% | 0.00% | A: 0.13% |
| 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 | 99.60% | 0.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1123252936 | ATCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACC -> GTCGGCGAGGTAGCTCTCGCCGACGACGTA GCAGCCGTTGTCCTCGACCTGGCGGCTGAC C | LOC_Os11g39060.1 | synonymous_variant ; p.Asp112Asp; LOW | synonymous_codon | Average:68.287; most accessible tissue: Callus, score: 83.174 | N | N | N | N |
| vg1123252936 | ATCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACC -> A | LOC_Os11g39060.1 | disruptive_inframe_deletion ; p.Glu92_Ala111del; MODERATE | inframe_variant | Average:68.287; most accessible tissue: Callus, score: 83.174 | N | N | N | N |