9 variations found. LOC_Os01g14730 (retrotransposon protein; putative; unclassified), ranging from 8,238,803 bp to 8,239,716 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0108238964 (J) | chr01 | 8238964 | G | T | 97.50% | 0.89% | G -> T | NA |
LOC_Os01g14730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g14730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 46.546; most accessible tissue: Minghui63 root, score: 63.193 |
| vg0108238993 (J) | chr01 | 8238993 | C | T | 98.10% | 0.89% | C -> T | NA |
LOC_Os01g14730.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g14730.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 46.361; most accessible tissue: Zhenshan97 flag leaf, score: 65.820 |
| vg0108239058 (J) | chr01 | 8239058 | G | A | 98.00% | 0.87% | G -> A | NA |
LOC_Os01g14720.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g14750.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g14730.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 47.460; most accessible tissue: Zhenshan97 flag leaf, score: 66.327 |
| vg0108239558 (J) | chr01 | 8239558 | T | C | 98.40% | 0.00% | T -> C | NA |
LOC_Os01g14730.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 46.991; most accessible tissue: Zhenshan97 flag leaf, score: 70.425 |
| vg0108239626 (J) | chr01 | 8239626 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os01g14730.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g14720.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 45.477; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 |
| vg0108239673 (J) | chr01 | 8239673 | C | T | 96.00% | 0.00% | C -> T | NA |
LOC_Os01g14730.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 43.495; most accessible tissue: Zhenshan97 flag leaf, score: 67.785 |
| vg0108239676 (J) | chr01 | 8239676 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os01g14730.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 43.561; most accessible tissue: Zhenshan97 flag leaf, score: 67.310 |
| vg0108239694 (J) | chr01 | 8239694 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os01g14730.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g14720.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g14750.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 44.367; most accessible tissue: Zhenshan97 flag leaf, score: 66.824 |
| vg0108239715 (J) | chr01 | 8239715 | G | A | 84.70% | 0.00% | G -> A |
LOC_Os01g14730.1 Alt: A| splice_region_variant&stop_retained_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 41.851; most accessible tissue: Zhenshan97 flag leaf, score: 63.670 |