16 variations found. Os06g0536600/LOC_Os06g34560 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 20,098,733 bp to 20,100,496 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os06g34560 | zinc finger, C3HC4 type domain containing protein; RAP ID: Os06g0536600; MSU ID: LOC_Os06g34560 |
The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0620098763 (J) | chr06 | 20098763 | T | C | 65.30% | 7.53% | C -> T | NA |
LOC_Os06g34560.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 95.755; most accessible tissue: Zhenshan97 flower, score: 98.276 |
| vg0620098852 (J) | chr06 | 20098852 | T | C | 47.40% | 7.87% | C -> T | NA |
LOC_Os06g34560.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.545; most accessible tissue: Zhenshan97 root, score: 98.164 |
| vg0620098865 (J) | chr06 | 20098865 | C | CACGT | 65.20% | 7.62% | CACGT -> C | NA |
LOC_Os06g34560.1 Alt: C| frameshift_variant&splice_donor_variant&splice_region_variant&intron_variant HIGH(snpEff)/splice_donor_variant(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 94.673; most accessible tissue: Zhenshan97 root, score: 98.199 |
| vg0620098962 (J) | chr06 | 20098962 | G | A | 75.10% | 7.60% | G -> A |
LOC_Os06g34550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34540.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34564.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 93.365; most accessible tissue: Zhenshan97 root, score: 97.626 |
|
| vg0620099096 (J) | chr06 | 20099096 | G | C | 84.20% | 7.41% | G -> C |
LOC_Os06g34550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 87.449; most accessible tissue: Zhenshan97 root, score: 96.054 |
|
| vg0620099120 (J) | chr06 | 20099120 | C | CGCA | 92.60% | 6.92% | C -> CGCA | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os06g34550.1 Alt: CGCA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34564.1 Alt: CGCA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: CGCA| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 86.446; most accessible tissue: Zhenshan97 root, score: 95.843 |
| vg0620099139 (J) | chr06 | 20099139 | C | T | 91.70% | 6.69% | C -> T | NA |
LOC_Os06g34550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 85.547; most accessible tissue: Zhenshan97 root, score: 95.586 |
| vg0620099286 (J) | chr06 | 20099286 | C | A | 47.30% | 7.96% | A -> C | NA |
LOC_Os06g34550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 81.044; most accessible tissue: Zhenshan97 root, score: 95.778 |
| vg0620099310 (J) | chr06 | 20099310 | G | C | 92.30% | 6.86% | G -> C | NA |
LOC_Os06g34550.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 79.030; most accessible tissue: Zhenshan97 root, score: 95.711 |
| vg0620099347 (J) | chr06 | 20099347 | G | A | 47.40% | 7.68% | A -> G | NA |
LOC_Os06g34550.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 76.996; most accessible tissue: Zhenshan97 root, score: 96.111 |
| vg0620099558 (J) | chr06 | 20099558 | C | T | 90.70% | 6.77% | C -> T | NA |
LOC_Os06g34550.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 66.899; most accessible tissue: Zhenshan97 root, score: 96.248 |
| vg0620099822 (J) | chr06 | 20099822 | G | A | 92.30% | 6.98% | G -> A | NA |
LOC_Os06g34550.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g34564.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g34560.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 55.199; most accessible tissue: Zhenshan97 root, score: 93.745 |
| vg0620100183 (J) | chr06 | 20100183 | G | A | 87.00% | 7.36% | G -> A | NA |
LOC_Os06g34560.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.444; most accessible tissue: Minghui63 root, score: 91.102 |
| vg0620100202 (J) | chr06 | 20100202 | G | A | 65.30% | 7.58% | A -> G | NA |
LOC_Os06g34560.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 76.862; most accessible tissue: Minghui63 root, score: 91.062 |
| vg0620100302 (J) | chr06 | 20100302 | A | T | 92.10% | 3.51% | A -> T | NA |
LOC_Os06g34560.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g34560.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 79.742; most accessible tissue: Minghui63 root, score: 92.615 |
| STR0620098866 (J) | chr06 | 20098866 | ACGTAC | ACGTACG TAC | 61.80% | 0.00% | ACGTACGTAC -> ACGTAC | NA |
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