14 variations found. LOC_Os02g44920 (protein kinase domain containing protein; expressed), ranging from 27,215,240 bp to 27,217,719 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0227215323 (J) | chr02 | 27215323 | GCGCCGC | GCGCCGC CGCCGC | 58.50% | 2.22% | GCGCCGC -> GCGCCGCCGC CGC,G | NA |
LOC_Os02g44920.1 Alt: GCGCCGCCGCCGC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os02g44920.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os02g44920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.279; most accessible tissue: Minghui63 flag leaf, score: 97.965 |
| vg0227215342 (J) | chr02 | 27215342 | CCCGT | C | 91.70% | 1.61% | CCCGT -> C,CGCCGT | NA |
LOC_Os02g44920.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g44920.1 Alt: CGCCGT| frameshift_variant HIGH(snpEff) LOC_Os02g44910.1 Alt: CGCCGT| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g44920.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 91.279; most accessible tissue: Minghui63 flag leaf, score: 98.029 |
| vg0227215553 (J) | chr02 | 27215553 | C | A | 63.50% | 0.00% | A -> C | NA |
LOC_Os02g44920.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 94.330; most accessible tissue: Minghui63 flag leaf, score: 98.473 |
| vg0227216029 (J) | chr02 | 27216029 | T | C | 63.50% | 0.02% | C -> T | NA |
LOC_Os02g44920.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g44920.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.268; most accessible tissue: Minghui63 flag leaf, score: 99.127 |
| vg0227216100 (J) | chr02 | 27216100 | T | C | 96.30% | 0.00% | T -> C |
LOC_Os02g44910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g44920.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 92.310; most accessible tissue: Minghui63 flag leaf, score: 99.018 |
|
| vg0227216190 (J) | chr02 | 27216190 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os02g44910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g44920.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 92.290; most accessible tissue: Minghui63 flag leaf, score: 98.240 |
| vg0227216192 (J) | chr02 | 27216192 | A | G | 90.90% | 0.23% | A -> G | NA |
LOC_Os02g44910.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g44920.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 92.379; most accessible tissue: Minghui63 flag leaf, score: 98.228 |
| vg0227216783 (J) | chr02 | 27216783 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os02g44910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os02g44920.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.873; most accessible tissue: Callus, score: 89.914 |
| vg0227216800 (J) | chr02 | 27216800 | T | C | 63.50% | 0.00% | C -> T | NA |
LOC_Os02g44910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g44920.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 69.046; most accessible tissue: Callus, score: 89.914 |
| vg0227217052 (J) | chr02 | 27217052 | A | C | 97.50% | 0.68% | A -> C | NA |
LOC_Os02g44920.1 Alt: DEL/splice_donor_variant(CooVar)
LOC_Os02g44920.1 Alt: C| splice_donor_variant&intron_variant HIGH(snpEff)/splice_donor_variant(CooVar) The average chromatin accessibility score: 76.291; most accessible tissue: Minghui63 flag leaf, score: 83.621 |
| vg0227217230 (J) | chr02 | 27217230 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os02g44920.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os02g44910.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 83.096; most accessible tissue: Zhenshan97 panicle, score: 89.389 |
| vg0227217420 (J) | chr02 | 27217420 | G | A | 63.50% | 0.00% | A -> G | NA |
LOC_Os02g44920.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.488; most accessible tissue: Zhenshan97 flag leaf, score: 88.363 |
| vg0227217457 (J) | chr02 | 27217457 | A | G | 99.70% | 0.00% | A -> G | NA |
LOC_Os02g44920.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os02g44910.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 81.598; most accessible tissue: Zhenshan97 flag leaf, score: 88.918 |
| vg0227217538 (J) | chr02 | 27217538 | A | C | 63.50% | 0.00% | C -> A | NA |
LOC_Os02g44910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g44920.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 80.196; most accessible tissue: Zhenshan97 flag leaf, score: 88.111 |