40 variations found. LOC_Os11g22800 (expressed protein), ranging from 13,116,731 bp to 13,117,208 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1113116732 (J) | chr11 | 13116732 | T | C | 50.70% | 8.57% | T -> C | NA |
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g22800.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar) The average chromatin accessibility score: 76.072; most accessible tissue: Minghui63 flag leaf, score: 94.503 |
| vg1113116758 (J) | chr11 | 13116758 | C | T | 98.80% | 0.80% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.831; most accessible tissue: Minghui63 flag leaf, score: 95.107 |
| vg1113116762 (J) | chr11 | 13116762 | G | A | 80.10% | 8.72% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.593; most accessible tissue: Minghui63 flag leaf, score: 94.850 |
| vg1113116763 (J) | chr11 | 13116763 | C | T | 87.70% | 8.00% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.710; most accessible tissue: Minghui63 flag leaf, score: 94.909 |
| vg1113116771 (J) | chr11 | 13116771 | G | Unkown | 99.10% | 0.85% | G -> T,A | NA |
LOC_Os11g22800.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os11g22790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff) LOC_Os11g22790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.577; most accessible tissue: Minghui63 flag leaf, score: 94.696 |
| vg1113116772 (J) | chr11 | 13116772 | C | T | 96.90% | 0.68% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.563; most accessible tissue: Minghui63 flag leaf, score: 94.696 |
| vg1113116782 (J) | chr11 | 13116782 | G | A | 96.50% | 0.00% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.491; most accessible tissue: Minghui63 flag leaf, score: 94.601 |
| vg1113116787 (J) | chr11 | 13116787 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g22790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.452; most accessible tissue: Minghui63 flag leaf, score: 94.569 |
| vg1113116798 (J) | chr11 | 13116798 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g22790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.316; most accessible tissue: Minghui63 flag leaf, score: 94.364 |
| vg1113116803 (J) | chr11 | 13116803 | C | T | 87.70% | 8.10% | C -> T,A | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g22800.1 Alt: A| stop_gained HIGH(snpEff) LOC_Os11g22790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.225; most accessible tissue: Minghui63 flag leaf, score: 94.258 |
| vg1113116806 (J) | chr11 | 13116806 | G | T | 96.40% | 0.63% | G -> T,A | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.168; most accessible tissue: Minghui63 flag leaf, score: 94.258 |
| vg1113116808 (J) | chr11 | 13116808 | C | A | 87.70% | 8.13% | C -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.090; most accessible tissue: Minghui63 flag leaf, score: 94.258 |
| vg1113116810 (J) | chr11 | 13116810 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g22790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 76.075; most accessible tissue: Minghui63 flag leaf, score: 94.221 |
| vg1113116812 (J) | chr11 | 13116812 | G | A | 87.70% | 8.06% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.022; most accessible tissue: Minghui63 flag leaf, score: 94.221 |
| vg1113116821 (J) | chr11 | 13116821 | G | A | 88.00% | 7.79% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.014; most accessible tissue: Minghui63 flag leaf, score: 94.147 |
| vg1113116824 (J) | chr11 | 13116824 | A | G | 83.90% | 8.95% | A -> G,T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g22800.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 75.520; most accessible tissue: Minghui63 flag leaf, score: 93.797 |
| vg1113116826 (J) | chr11 | 13116826 | T | G | 87.50% | 7.81% | T -> G | NA |
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g22800.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 75.447; most accessible tissue: Minghui63 flag leaf, score: 93.797 |
| vg1113116834 (J) | chr11 | 13116834 | G | A | 99.60% | 0.00% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os11g22790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 75.338; most accessible tissue: Minghui63 flag leaf, score: 93.416 |
| vg1113116838 (J) | chr11 | 13116838 | C | T | 75.50% | 17.94% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.480; most accessible tissue: Minghui63 flag leaf, score: 93.546 |
| vg1113116839 (J) | chr11 | 13116839 | G | A | 73.50% | 18.11% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 75.480; most accessible tissue: Minghui63 flag leaf, score: 93.546 |
| vg1113116843 (J) | chr11 | 13116843 | G | C | 64.80% | 18.96% | G -> C | NA |
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g22800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 75.588; most accessible tissue: Minghui63 flag leaf, score: 93.503 |
| vg1113116918 (J) | chr11 | 13116918 | T | G | 34.50% | 49.09% | T -> G | NA |
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g22800.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 73.585; most accessible tissue: Minghui63 flag leaf, score: 92.689 |
| vg1113116921 (J) | chr11 | 13116921 | A | G | 34.40% | 52.45% | A -> G | NA |
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g22800.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 73.220; most accessible tissue: Minghui63 flag leaf, score: 92.472 |
| vg1113116937 (J) | chr11 | 13116937 | G | A | 99.70% | 0.00% | G -> A,T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g22790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os11g22790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.676; most accessible tissue: Minghui63 flag leaf, score: 91.758 |
| vg1113117000 (J) | chr11 | 13117000 | G | A | 78.30% | 12.48% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 66.183; most accessible tissue: Minghui63 young leaf, score: 87.217 |
| vg1113117065 (J) | chr11 | 13117065 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os11g22790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.916; most accessible tissue: Minghui63 young leaf, score: 80.234 |
| vg1113117105 (J) | chr11 | 13117105 | C | A | 75.60% | 14.05% | C -> A,T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os11g22790.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 60.946; most accessible tissue: Minghui63 flower, score: 85.195 |
| vg1113117135 (J) | chr11 | 13117135 | C | T | 65.90% | 8.76% | T -> C,A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os11g22790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g22800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 64.240; most accessible tissue: Minghui63 flag leaf, score: 88.687 |
| vg1113117138 (J) | chr11 | 13117138 | C | T | 68.90% | 17.65% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 65.320; most accessible tissue: Minghui63 flag leaf, score: 89.121 |
| vg1113117146 (J) | chr11 | 13117146 | G | A | 82.10% | 1.29% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 64.891; most accessible tissue: Minghui63 flag leaf, score: 89.224 |
| vg1113117152 (J) | chr11 | 13117152 | G | A | 98.60% | 0.00% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.488; most accessible tissue: Minghui63 flag leaf, score: 87.594 |
| vg1113117158 (J) | chr11 | 13117158 | T | G | 99.80% | 0.00% | T -> G | NA |
LOC_Os11g22800.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os11g22790.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 63.673; most accessible tissue: Minghui63 flag leaf, score: 87.980 |
| vg1113117164 (J) | chr11 | 13117164 | C | T | 99.00% | 0.02% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.470; most accessible tissue: Minghui63 flag leaf, score: 87.854 |
| vg1113117165 (J) | chr11 | 13117165 | G | A | 74.70% | 15.30% | G -> A,T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.600; most accessible tissue: Minghui63 flag leaf, score: 87.854 |
| vg1113117172 (J) | chr11 | 13117172 | C | T | 71.00% | 18.54% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 63.938; most accessible tissue: Minghui63 flag leaf, score: 88.459 |
| vg1113117182 (J) | chr11 | 13117182 | C | T | 99.00% | 0.83% | C -> T | NA |
LOC_Os11g22800.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 64.410; most accessible tissue: Minghui63 flag leaf, score: 88.574 |
| vg1113117183 (J) | chr11 | 13117183 | G | A | 98.90% | 0.00% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 64.638; most accessible tissue: Minghui63 flag leaf, score: 88.907 |
| vg1113117187 (J) | chr11 | 13117187 | G | A | 97.00% | 1.84% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g22800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 64.728; most accessible tissue: Minghui63 flag leaf, score: 88.907 |
| vg1113117203 (J) | chr11 | 13117203 | G | A | 98.80% | 0.00% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 66.578; most accessible tissue: Minghui63 flag leaf, score: 89.425 |
| vg1113117204 (J) | chr11 | 13117204 | G | Unkown | 99.70% | 0.13% | G -> A | NA |
LOC_Os11g22800.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os11g22790.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 66.886; most accessible tissue: Minghui63 flag leaf, score: 89.425 |