| Variant ID: vg1201715496 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 1715496 |
| Reference Allele: G | Alternative Allele: GGTGATGGTCGTGGTGGTGAT,GGTGATGGTCGTGGTGGTGATATCGTCGTCCTC |
| Primary Allele: G | Secondary Allele: GGTGATGGTCGTGGTGGTGA T |
Inferred Ancestral Allele: Not determined.
AGAGTTCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGCC[G/GGTGATGGTCGTGGTGGTGAT,GGTGATGGTCGTGGTGGTGATATCGTCGTCCTC]
ACGGGGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCA
TGAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCCCCGT[C/ATCACCACCACGACCATCACC,GAGGACGACGATATCACCACCACGACCATCACC]
GGCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGAACTCT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GGTGATGGTCGTGGTGGTGA T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 46.10% | 1.00% | 8.65% | 44.20% | GGTGATGGTCGTGGTGGTGATATCGTCGTCCTC: 0.02% |
| All Indica | 2759 | 11.90% | 1.70% | 13.85% | 72.53% | GGTGATGGTCGTGGTGGTGATATCGTCGTCCTC: 0.04% |
| All Japonica | 1512 | 97.30% | 0.10% | 0.33% | 2.25% | NA |
| Aus | 269 | 83.30% | 0.00% | 6.32% | 10.41% | NA |
| Indica I | 595 | 3.50% | 0.50% | 13.45% | 82.52% | NA |
| Indica II | 465 | 8.40% | 2.40% | 16.56% | 72.69% | NA |
| Indica III | 913 | 15.40% | 2.00% | 7.56% | 74.92% | GGTGATGGTCGTGGTGGTGATATCGTCGTCCTC: 0.11% |
| Indica Intermediate | 786 | 16.30% | 1.80% | 19.85% | 62.09% | NA |
| Temperate Japonica | 767 | 95.70% | 0.30% | 0.39% | 3.65% | NA |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.20% | 0.99% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 68.90% | 0.00% | 5.56% | 25.56% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715496 | G -> GGTGATGGTCGTGGTGGTGATATCGTCGTC CTC | LOC_Os12g04090.1 | frameshift_variant ; p.Thr108fs; HIGH | frameshift_variant | Average:70.833; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715496 | G -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:70.833; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715496 | G -> GGTGATGGTCGTGGTGGTGAT | LOC_Os12g04090.1 | frameshift_variant ; p.Thr108fs; HIGH | frameshift_variant | Average:70.833; most accessible tissue: Callus, score: 91.31 | N | N | N | N |