7 variations found. LOC_Os11g35130 (transposon protein; putative; CACTA; En%2FSpm sub-class), ranging from 20,595,119 bp to 20,598,275 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1120595800 (J) | chr11 | 20595800 | GTGGTA | G | 29.20% | 65.28% | GTGGTA -> G | NA |
LOC_Os11g35130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g35130.1 Alt: G| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 6.395; most accessible tissue: Callus, score: 17.269 |
| vg1120596229 (J) | chr11 | 20596229 | G | A | 30.00% | 65.17% | G -> A | NA |
LOC_Os11g35130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g35130.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.970; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1120596236 (J) | chr11 | 20596236 | C | T | 29.80% | 64.66% | C -> T | NA |
LOC_Os11g35130.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g35130.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.970; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg1120597012 (J) | chr11 | 20597012 | A | G | 10.10% | 66.89% | G -> A | NA |
LOC_Os11g35130.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g35130.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.371; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1120597392 (J) | chr11 | 20597392 | T | TA | 27.50% | 42.85% | T -> TA | NA |
LOC_Os11g35140.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g35130.1 Alt: TA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.067; most accessible tissue: Zhenshan97 flag leaf, score: 17.069 |
| vg1120598096 (J) | chr11 | 20598096 | G | A | 33.30% | 58.93% | G -> A | NA |
LOC_Os11g35130.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g35130.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1120598158 (J) | chr11 | 20598158 | T | C | 34.80% | 59.50% | T -> C | NA |
LOC_Os11g35130.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g35130.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |