| Variant ID: vg1201715497 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr12 | Position: 1715497 |
| Reference Allele: A | Alternative Allele: ATGGT,ATGGTCGTGGTGGTGATAT,ATGGTCGTGGTGGTGATATCGT,ATGGTCGTGGTGGTGATATCGTCGTGCT |
| Primary Allele: A | Secondary Allele: ATGGTCGTGGTGGTGATATC GT |
Inferred Ancestral Allele: Not determined.
GAGTTCCGTCGAGGGGTGTACCAGGGAGAGGTGTACTGGGCTGGCCGAGTGATCAGGCCTCGTCCTTCGCCCATGCTAGGACGACGTCGCCGCGCCGCCG[A/ATGGT,ATGGTCGTGGTGGTGATAT,ATGGTCGTGGTGGTGATATCGT,ATGGTCGTGGTGGTGATATCGTCGTGCT]
CGGGGATGCCCCGATGCAAGATGTCGCGAGATGTCCTCCTGGGCCTCGCGCTGACGAAGGCGTGCGACGCGAGGCAGGAGGAGTGCGCCGTGTGCCTCAG
CTGAGGCACACGGCGCACTCCTCCTGCCTCGCGTCGCACGCCTTCGTCAGCGCGAGGCCCAGGAGGACATCTCGCGACATCTTGCATCGGGGCATCCCCG[T/ACCAT,ATATCACCACCACGACCAT,ACGATATCACCACCACGACCAT,AGCACGACGATATCACCACCACGACCAT]
CGGCGGCGCGGCGACGTCGTCCTAGCATGGGCGAAGGACGAGGCCTGATCACTCGGCCAGCCCAGTACACCTCTCCCTGGTACACCCCTCGACGGAACTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of ATGGTCGTGGTGGTGATATC GT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 45.00% | 2.60% | 12.72% | 35.61% | ATGGT: 2.14%; ATGGTCGTGGTGGTGATAT: 1.90%; ATGGTCGTGGTGGTGATATCGTCGTGCT: 0.02% |
| All Indica | 2759 | 10.20% | 4.10% | 20.51% | 58.39% | ATGGT: 3.55%; ATGGTCGTGGTGGTGATAT: 3.15%; ATGGTCGTGGTGGTGATATCGTCGTGCT: 0.04% |
| All Japonica | 1512 | 97.20% | 0.30% | 0.79% | 1.65% | ATGGTCGTGGTGGTGATAT: 0.07% |
| Aus | 269 | 82.20% | 1.50% | 5.20% | 10.04% | ATGGTCGTGGTGGTGATAT: 0.74%; ATGGT: 0.37% |
| Indica I | 595 | 2.20% | 2.70% | 23.36% | 67.39% | ATGGTCGTGGTGGTGATAT: 2.52%; ATGGT: 1.85% |
| Indica II | 465 | 6.70% | 3.90% | 22.58% | 61.51% | ATGGT: 3.23%; ATGGTCGTGGTGGTGATAT: 2.15% |
| Indica III | 913 | 13.30% | 5.80% | 15.12% | 56.19% | ATGGT: 5.15%; ATGGTCGTGGTGGTGATAT: 4.38%; ATGGTCGTGGTGGTGATATCGTCGTGCT: 0.11% |
| Indica Intermediate | 786 | 14.90% | 3.40% | 23.41% | 52.29% | ATGGT: 3.18%; ATGGTCGTGGTGGTGATAT: 2.80% |
| Temperate Japonica | 767 | 95.60% | 0.50% | 1.17% | 2.61% | ATGGTCGTGGTGGTGATAT: 0.13% |
| Tropical Japonica | 504 | 98.80% | 0.00% | 0.60% | 0.60% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 96.90% | 1.00% | 0.00% | 2.08% | NA |
| Intermediate | 90 | 67.80% | 0.00% | 10.00% | 20.00% | ATGGT: 2.22% |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1201715497 | A -> ATGGT | LOC_Os12g04090.1 | frameshift_variant ; p.Thr108fs; HIGH | frameshift_variant | Average:70.894; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715497 | A -> ATGGTCGTGGTGGTGATAT | LOC_Os12g04090.1 | disruptive_inframe_insertion ; p.Thr108delinsMetValValValValI leSer; MODERATE | inframe_variant | Average:70.894; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715497 | A -> DEL | LOC_Os12g04090.1 | N | frameshift_variant | Average:70.894; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715497 | A -> ATGGTCGTGGTGGTGATATCGT | LOC_Os12g04090.1 | disruptive_inframe_insertion ; p.Thr108delinsMetValValValValI leSerSer; MODERATE | inframe_variant | Average:70.894; most accessible tissue: Callus, score: 91.31 | N | N | N | N |
| vg1201715497 | A -> ATGGTCGTGGTGGTGATATCGTCGTGCT | LOC_Os12g04090.1 | disruptive_inframe_insertion ; p.Thr108delinsMetValValValValI leSerSerCysSer; MODERATE | inframe_variant | Average:70.894; most accessible tissue: Callus, score: 91.31 | N | N | N | N |