| Variant ID: vg1105183880 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183880 |
| Reference Allele: G | Alternative Allele: GCAT,GCATGAGTAGCTTAAGCTTT |
| Primary Allele: G | Secondary Allele: GCATGAGTAGCTTAAGCTTT |
Inferred Ancestral Allele: Not determined.
ATTCACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAG[G/GCAT,GCATGAGTAGCTTAAGCTTT]
GGCTGTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTC
GAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAACAGCC[C/ATGC,AAAGCTTAAGCTACTCATGC]
CTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGTGAAT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of GCATGAGTAGCTTAAGCTTT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 9.90% | 2.70% | 13.67% | 71.60% | GCAT: 2.14% |
| All Indica | 2759 | 0.80% | 2.00% | 9.82% | 85.72% | GCAT: 1.63% |
| All Japonica | 1512 | 28.00% | 4.00% | 20.04% | 44.97% | GCAT: 2.98% |
| Aus | 269 | 0.70% | 3.30% | 16.73% | 75.46% | GCAT: 3.72% |
| Indica I | 595 | 2.00% | 1.00% | 2.35% | 94.45% | GCAT: 0.17% |
| Indica II | 465 | 0.40% | 0.60% | 4.73% | 93.55% | GCAT: 0.65% |
| Indica III | 913 | 0.20% | 3.70% | 16.98% | 75.79% | GCAT: 3.29% |
| Indica Intermediate | 786 | 0.90% | 1.50% | 10.18% | 86.01% | GCAT: 1.40% |
| Temperate Japonica | 767 | 33.40% | 3.00% | 22.16% | 39.24% | GCAT: 2.22% |
| Tropical Japonica | 504 | 14.10% | 6.20% | 14.68% | 60.52% | GCAT: 4.56% |
| Japonica Intermediate | 241 | 39.80% | 2.90% | 24.48% | 30.71% | GCAT: 2.07% |
| VI/Aromatic | 96 | 4.20% | 3.10% | 14.58% | 77.08% | GCAT: 1.04% |
| Intermediate | 90 | 16.70% | 0.00% | 14.44% | 68.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183880 | G -> GCAT | LOC_Os11g09710.1 | inframe_insertion ; p.Arg318_Gly319insHis; MODERATE | inframe_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183880 | G -> GCATGAGTAGCTTAAGCTTT | LOC_Os11g09710.1 | frameshift_variant&stop_gained ; p.Gly319fs; HIGH | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183880 | G -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |