3 variations found. LOC_Os11g02250 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 641,560 bp to 641,998 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1100641589 (J) | chr11 | 641589 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os11g02250.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os11g02260.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 79.698; most accessible tissue: Minghui63 young leaf, score: 90.630 |
| vg1100641805 (J) | chr11 | 641805 | T | C | 83.60% | 0.00% | T -> C | NA |
LOC_Os11g02250.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 86.579; most accessible tissue: Minghui63 young leaf, score: 92.617 |
| vg1100641881 (J) | chr11 | 641881 | G | A | 98.10% | 0.00% | G -> A | NA |
LOC_Os11g02250.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.878; most accessible tissue: Minghui63 panicle, score: 91.919 |