6 variations found. LOC_Os11g04280 (zinc finger; C3HC4 type domain containing protein), ranging from 1,752,233 bp to 1,752,890 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Color | Explain | Details |
|---|---|---|
| red | High impact variants defined by snpEff | 'STOP_LOST', 'START_LOST', 'STOP_GAINED', 'FRAME_SHIFT' et. al., the details can be found at http://snpef f.sourceforge.net/SnpEff_manual.html#eff. |
| purple | 'Damaging' or 'probably damaging' non-synonymous SNPs defined by PolyPhen-2 | This is a qualitative result of nonsynonymous SNP annotation, where 'damaging' or 'probably damaging' means that the variant is more likely to affect protein function. Details can be found here. |
| Var ID | Chrom | Position | Primary Allele | Secondary Allele | Primary Allele Frequency | DEL Frequency | Var | GWAS Results | Effect |
|---|---|---|---|---|---|---|---|---|---|
| vg1101752255 (J) | chr11 | 1752255 | C | A | 99.60% | 0.00% | C -> A | NA |
LOC_Os11g04280.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os11g04270.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04240.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04267.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 43.426; most accessible tissue: Callus, score: 67.863 |
| vg1101752260 (J) | chr11 | 1752260 | TG | T | 99.80% | 0.00% | TG -> T | NA |
LOC_Os11g04280.1 Alt: T| frameshift_variant HIGH(snpEff)
LOC_Os11g04270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04267.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 41.824; most accessible tissue: Callus, score: 67.863 |
| vg1101752360 (J) | chr11 | 1752360 | CCTGT | C | 99.70% | 0.00% | CCTGT -> C | NA |
LOC_Os11g04280.1 Alt: C| frameshift_variant HIGH(snpEff)
LOC_Os11g04270.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04240.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 24.657; most accessible tissue: Zhenshan97 flower, score: 43.307 |
| vg1101752503 (J) | chr11 | 1752503 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os11g04280.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g04270.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g04240.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os11g04267.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 17.422; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg1101752536 (J) | chr11 | 1752536 | G | T | 66.80% | 0.00% | T -> G | NA |
LOC_Os11g04280.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 15.842; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg1101752685 (J) | chr11 | 1752685 | A | G | 0.30% | 96.42% | G -> A | NA |
LOC_Os11g04280.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g04280.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.736; most accessible tissue: Zhenshan97 flower, score: 15.748 |