| Variant ID: vg1105183885 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183885 |
| Reference Allele: G | Alternative Allele: GC,C |
| Primary Allele: G | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
CATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGCT[G/GC,C]
TTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCCATAT
ATATGGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAA[C/GC,G]
AGCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 9.90% | 0.40% | 7.38% | 81.85% | GC: 0.40% |
| All Indica | 2759 | 0.90% | 0.40% | 5.04% | 93.51% | GC: 0.14% |
| All Japonica | 1512 | 28.00% | 0.30% | 9.59% | 61.38% | GC: 0.73% |
| Aus | 269 | 0.70% | 1.10% | 21.19% | 75.46% | GC: 1.49% |
| Indica I | 595 | 2.40% | 0.50% | 0.50% | 96.47% | GC: 0.17% |
| Indica II | 465 | 0.40% | 0.20% | 1.29% | 98.06% | NA |
| Indica III | 913 | 0.20% | 0.50% | 11.17% | 88.06% | NA |
| Indica Intermediate | 786 | 0.90% | 0.30% | 3.56% | 94.91% | GC: 0.38% |
| Temperate Japonica | 767 | 33.50% | 0.30% | 13.30% | 52.41% | GC: 0.52% |
| Tropical Japonica | 504 | 14.10% | 0.60% | 1.79% | 82.14% | GC: 1.39% |
| Japonica Intermediate | 241 | 39.40% | 0.00% | 14.11% | 46.47% | NA |
| VI/Aromatic | 96 | 4.20% | 1.00% | 4.17% | 90.62% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 4.44% | 77.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183885 | G -> GC | LOC_Os11g09710.1 | frameshift_variant ; p.Leu321fs; HIGH | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183885 | G -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183885 | G -> C | LOC_Os11g09710.1 | missense_variant ; p.Cys320Ser; MODERATE | nonsynonymous_codon ; C320S | Average:19.337; most accessible tissue: Callus, score: 53.099 | unknown | unknown | DELETERIOUS | 0.00 |