| Variant ID: vg1123253223 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr11 | Position: 23253223 |
| Reference Allele: C | Alternative Allele: CCGT,T |
| Primary Allele: C | Secondary Allele: CCGT |
Inferred Ancestral Allele: Not determined.
CTCTCGAACGCCAGGATGGAGTCGACGTACCCCTGCGCCAATAATGGCGCAACGGCGGCTGGCTTCTGCGGCTCGCCGGCGGCGGTGGCGGCCGCCGCCG[C/CCGT,T]
CGTCGTCTTCTTTGCCTCGTCGGCTGATGCCACCGCAGAGGCGTCCATGGATGATGGATCAGTATTCACTTGGAGTGCGTATGTCGACGAACTCGGTTGC
GCAACCGAGTTCGTCGACATACGCACTCCAAGTGAATACTGATCCATCATCCATGGACGCCTCTGCGGTGGCATCAGCCGACGAGGCAAAGAAGACGACG[G/ACGG,A]
CGGCGGCGGCCGCCACCGCCGCCGGCGAGCCGCAGAAGCCAGCCGCCGTTGCGCCATTATTGGCGCAGGGGTACGTCGACTCCATCCTGGCGTTCGAGAG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CCGT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 97.70% | 2.30% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 96.30% | 3.70% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 94.70% | 5.30% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 94.10% | 5.90% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1123253223 | C -> CCGT | LOC_Os11g39060.1 | inframe_insertion ; p.Thr16dup; MODERATE | inframe_variant | Average:69.352; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253223 | C -> T | LOC_Os11g39060.1 | missense_variant ; p.Ala17Thr; MODERATE | N | Average:69.352; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253223 | C -> T | LOC_Os11g39040.1 | upstream_gene_variant ; 4280.0bp to feature; MODIFIER | N | Average:69.352; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253223 | C -> T | LOC_Os11g39050.1 | upstream_gene_variant ; 2708.0bp to feature; MODIFIER | N | Average:69.352; most accessible tissue: Callus, score: 82.581 | N | N | N | N |
| vg1123253223 | C -> T | LOC_Os11g39070.1 | downstream_gene_variant ; 2563.0bp to feature; MODIFIER | N | Average:69.352; most accessible tissue: Callus, score: 82.581 | N | N | N | N |