| Variant ID: vg1105183894 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 5183894 |
| Reference Allele: C | Alternative Allele: CTGG |
| Primary Allele: C | Secondary Allele: CTGG |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.06, others allele: 0.00, population size: 49. )
AAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGCTGTTTGGTTT[C/CTGG]
CAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCCATATCCTTGGACT
AGTCCAAGGATATGGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTG[G/CCAG]
AAACCAAACAGCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTT
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CTGG(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.10% | 0.30% | 3.98% | 85.63% | NA |
| All Indica | 2759 | 0.90% | 0.10% | 4.20% | 94.71% | NA |
| All Japonica | 1512 | 28.20% | 0.50% | 3.37% | 67.86% | NA |
| Aus | 269 | 0.70% | 1.50% | 5.58% | 92.19% | NA |
| Indica I | 595 | 2.50% | 0.20% | 0.34% | 96.97% | NA |
| Indica II | 465 | 0.40% | 0.00% | 0.22% | 99.35% | NA |
| Indica III | 913 | 0.10% | 0.00% | 9.64% | 90.25% | NA |
| Indica Intermediate | 786 | 1.00% | 0.40% | 3.18% | 95.42% | NA |
| Temperate Japonica | 767 | 33.80% | 0.50% | 1.96% | 63.75% | NA |
| Tropical Japonica | 504 | 14.10% | 0.80% | 1.19% | 83.93% | NA |
| Japonica Intermediate | 241 | 40.20% | 0.00% | 12.45% | 47.30% | NA |
| VI/Aromatic | 96 | 4.20% | 0.00% | 3.12% | 92.71% | NA |
| Intermediate | 90 | 17.80% | 0.00% | 3.33% | 78.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105183894 | C -> CTGG | LOC_Os11g09710.1 | disruptive_inframe_insertion ; p.Ser323_Arg324insGly; MODERATE | inframe_variant | Average:19.676; most accessible tissue: Callus, score: 53.099 | N | N | N | N |
| vg1105183894 | C -> DEL | LOC_Os11g09710.1 | N | frameshift_variant | Average:19.676; most accessible tissue: Callus, score: 53.099 | N | N | N | N |