| Variant ID: vg1105183884 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183884 |
| Reference Allele: T | Alternative Allele: TTAA |
| Primary Allele: T | Secondary Allele: TTAA |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, others allele: 0.00, population size: 49. )
ACATGGGACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGC[T/TTAA]
GTTTGGTTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCCATA
TATGGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAACCAAAC[A/TTAA]
GCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTCCCATGT
| Populations | Population Size | Frequency of T(primary allele) | Frequency of TTAA(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 9.90% | 0.40% | 3.17% | 86.46% | NA |
| All Indica | 2759 | 0.90% | 0.10% | 3.70% | 95.29% | NA |
| All Japonica | 1512 | 28.00% | 0.80% | 2.05% | 69.18% | NA |
| Aus | 269 | 0.70% | 1.50% | 4.09% | 93.68% | NA |
| Indica I | 595 | 2.40% | 0.20% | 0.34% | 97.14% | NA |
| Indica II | 465 | 0.40% | 0.00% | 0.22% | 99.35% | NA |
| Indica III | 913 | 0.20% | 0.00% | 8.32% | 91.46% | NA |
| Indica Intermediate | 786 | 0.80% | 0.40% | 2.93% | 95.93% | NA |
| Temperate Japonica | 767 | 33.40% | 0.70% | 0.52% | 65.45% | NA |
| Tropical Japonica | 504 | 14.10% | 1.40% | 0.60% | 83.93% | NA |
| Japonica Intermediate | 241 | 39.80% | 0.00% | 9.96% | 50.21% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 4.17% | 91.67% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 2.22% | 78.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183884 | T -> TTAA | LOC_Os11g09710.1 | disruptive_inframe_insertion ; p.Cys320delinsLeuSer; MODERATE | inframe_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183884 | T -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:19.337; most accessible tissue: Callus, score: 53.099 | N | N | N | N |