| Variant ID: vg1105183811 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183811 |
| Reference Allele: T | Alternative Allele: TGGGAG,TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCC,TGG,TGGGAGAATTTACTCTATGCCACTCTACC,TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGC,TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCCAAATGCC |
| Primary Allele: T | Secondary Allele: TGG |
Inferred Ancestral Allele: Not determined.
CGATTACATTGATTGGATCTGGGTTGGCTTCTAAGAACAATATGCCTGAGACGTTCTATTCAGCCAGAGATTCACATGGGACTAAATCCCATCCTGACCA[T/TGGGAG,TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCC,TGG,TGGGAGAATTTACTCTATGCCACTCTACC,TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGC,TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCCAAATGCC]
AAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGCTGTTTGGTTTCCAGGGACTTATTCCAAT
ATTGGAATAAGTCCCTGGAAACCAAACAGCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTT[A/CTCCCA,GGGAACTGCCATTTTGGTAGAGTGGCATAGAGTAAATTCTCCCA,CCA,GGTAGAGTGGCATAGAGTAAATTCTCCCA,GCCATTTTGGTAGAGTGGCATAGAGTAAATTCTCCCA,GGCATTTGGGAACTGCCATTTTGGTAGAGTGGCATAGAGTAAATTCTCCCA]
TGGTCAGGATGGGATTTAGTCCCATGTGAATCTCTGGCTGAATAGAACGTCTCAGGCATATTGTTCTTAGAAGCCAACCCAGATCCAATCAATGTAATCG
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.60% | 0.30% | 2.56% | 30.19% | TGGGAGAATTTACTCTATGCCACTCTACC: 0.17%; TGGGAG: 0.08%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCC: 0.06%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGC: 0.06%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCCAAATGCC: 0.04% |
| All Indica | 2759 | 50.60% | 0.00% | 2.28% | 47.01% | TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCCAAATGCC: 0.04%; TGGGAGAATTTACTCTATGCCACTCTACC: 0.04% |
| All Japonica | 1512 | 96.20% | 0.30% | 2.12% | 1.06% | TGGGAGAATTTACTCTATGCCACTCTACC: 0.26%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCC: 0.07%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGC: 0.07% |
| Aus | 269 | 64.70% | 0.00% | 4.09% | 29.74% | TGGGAGAATTTACTCTATGCCACTCTACC: 0.74%; TGGGAG: 0.37%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCCAAATGCC: 0.37% |
| Indica I | 595 | 27.90% | 0.00% | 4.37% | 67.73% | NA |
| Indica II | 465 | 22.40% | 0.00% | 3.01% | 74.62% | NA |
| Indica III | 913 | 73.10% | 0.00% | 1.10% | 25.85% | NA |
| Indica Intermediate | 786 | 58.50% | 0.00% | 1.65% | 39.57% | TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCCAAATGCC: 0.13%; TGGGAGAATTTACTCTATGCCACTCTACC: 0.13% |
| Temperate Japonica | 767 | 94.80% | 0.40% | 2.61% | 1.83% | TGGGAGAATTTACTCTATGCCACTCTACC: 0.26%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGC: 0.13% |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 92.50% | 0.40% | 4.98% | 0.83% | TGGGAGAATTTACTCTATGCCACTCTACC: 0.83%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCC: 0.41% |
| VI/Aromatic | 96 | 62.50% | 7.30% | 13.54% | 8.33% | TGGGAG: 3.12%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCC: 2.08%; TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGC: 2.08%; TGGGAGAATTTACTCTATGCCACTCTACC: 1.04% |
| Intermediate | 90 | 67.80% | 1.10% | 2.22% | 28.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183811 | T -> TGGGAGAATTTACTCTATGCCACTCTACCA AAATGGCAGTTCCC | LOC_Os11g09710.1 | frameshift_variant ; p.Lys296fs; HIGH | frameshift_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183811 | T -> TGG | LOC_Os11g09710.1 | frameshift_variant ; p.Lys296fs; HIGH | frameshift_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183811 | T -> TGGGAGAATTTACTCTATGCCACTCTACCA AAATGGC | LOC_Os11g09710.1 | inframe_insertion ; p.His295_Lys296insGlyArgIleTyr SerMetProLeuTyrGlnAsnGly; MODERATE | inframe_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183811 | T -> TGGGAG | LOC_Os11g09710.1 | frameshift_variant ; p.Lys296fs; HIGH | frameshift_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183811 | T -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183811 | T -> TGGGAGAATTTACTCTATGCCACTCTACC | LOC_Os11g09710.1 | frameshift_variant ; p.Lys296fs; HIGH | frameshift_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |
| vg1105183811 | T -> TGGGAGAATTTACTCTATGCCACTCTACCA AAATGGCAGTTCCCAAATGCC | LOC_Os11g09710.1 | frameshift_variant ; p.Lys296fs; HIGH | frameshift_variant | Average:18.184; most accessible tissue: Callus, score: 89.679 | N | N | N | N |