| Variant ID: vg0233325754 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr02 | Position: 33325754 |
| Reference Allele: GTCGTCGTCGTCT | Alternative Allele: G |
| Primary Allele: GTCGTCGTCGTCT | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
GCAGCAGCACCAGCGCCTTGCTTGACGCCGACAGCTTGGGGAAGCCATGCTTAGAGCTCTTCGCCGGCGGCATGGCAGGCAAGAGCTCGAGCTCGACACA[GTCGTCGTCGTCT/G]
TCGTCGTCGTTGCTGCTGCGATTCAAGAAGCTCTCCTTGTGATCCAGAGATTGCTGTGAATTGAATTGTAAATGCGTGCAATTGGGTGGCGCGAGTGATA
TATCACTCGCGCCACCCAATTGCACGCATTTACAATTCAATTCACAGCAATCTCTGGATCACAAGGAGAGCTTCTTGAATCGCAGCAGCAACGACGACGA[AGACGACGACGAC/C]
TGTGTCGAGCTCGAGCTCTTGCCTGCCATGCCGCCGGCGAAGAGCTCTAAGCATGGCTTCCCCAAGCTGTCGGCGTCAAGCAAGGCGCTGGTGCTGCTGC
| Populations | Population Size | Frequency of GTCGTCGTCGTCT(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.80% | 0.20% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 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 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233325754 | GTCGTCGTCGTCT -> G | LOC_Os02g54370.1 | disruptive_inframe_deletion ; p.Glu53_Asp56del; MODERATE | N | Average:64.002; most accessible tissue: Callus, score: 81.364 | N | N | N | N |
| vg0233325754 | GTCGTCGTCGTCT -> G | LOC_Os02g54360.1 | upstream_gene_variant ; 3216.0bp to feature; MODIFIER | N | Average:64.002; most accessible tissue: Callus, score: 81.364 | N | N | N | N |
| vg0233325754 | GTCGTCGTCGTCT -> G | LOC_Os02g54390.1 | downstream_gene_variant ; 4754.0bp to feature; MODIFIER | N | Average:64.002; most accessible tissue: Callus, score: 81.364 | N | N | N | N |