9 variations found. LOC_Os11g22320 (retrotransposon; putative; centromere-specific), ranging from 12,794,788 bp to 12,795,501 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1112794815 (J) | chr11 | 12794815 | T | A | 32.90% | 31.55% | T -> A | NA |
LOC_Os11g22320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g22320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.159; most accessible tissue: Zhenshan97 flag leaf, score: 14.027 |
| vg1112794832 (J) | chr11 | 12794832 | G | A | 31.70% | 31.38% | G -> A,T | NA |
LOC_Os11g22320.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g22320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os11g22320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.975; most accessible tissue: Zhenshan97 flag leaf, score: 15.873 |
| vg1112794841 (J) | chr11 | 12794841 | T | C | 36.00% | 31.19% | T -> C | NA |
LOC_Os11g22320.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g22320.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.316; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 |
| vg1112794952 (J) | chr11 | 12794952 | A | C | 35.80% | 15.87% | A -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g22310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g22330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g22320.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 9.614; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 |
| vg1112795017 (J) | chr11 | 12795017 | C | T | 34.30% | 25.77% | C -> T | NA |
LOC_Os11g22310.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g22330.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g22320.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 9.702; most accessible tissue: Zhenshan97 flag leaf, score: 17.677 |
| vg1112795069 (J) | chr11 | 12795069 | T | C | 35.20% | 35.67% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g22310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g22330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g22320.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 9.396; most accessible tissue: Zhenshan97 flag leaf, score: 15.278 |
| vg1112795322 (J) | chr11 | 12795322 | T | C | 32.40% | 25.92% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g22310.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g22330.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g22320.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.993; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg1112795401 (J) | chr11 | 12795401 | G | A | 34.40% | 30.32% | G -> A | NA |
LOC_Os11g22320.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g22320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.266; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg1112795436 (J) | chr11 | 12795436 | G | A | 34.20% | 46.93% | G -> A | NA |
LOC_Os11g22320.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g22320.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.193; most accessible tissue: Callus, score: 42.724 |