13 variations found. Os07g0179300/LOC_Os07g08200 (methyltransferase domain containing protein; putative; expressed), ranging from 4,182,043 bp to 4,184,048 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os07g08200 | methyltransferase domain containing protein, putative, expressed; RAP ID: Os07g0179300; MSU ID: LOC_Os07g08200 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0704183109 (J) | chr07 | 4183109 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os07g08190.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.3 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.2 Alt: C| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08200.1 Alt: C| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 57.792; most accessible tissue: Minghui63 flag leaf, score: 76.091 |
| vg0704183155 (J) | chr07 | 4183155 | GA | GAA | 99.80% | 0.00% | GA -> G,GAA | NA |
LOC_Os07g08190.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08210.1 Alt: GAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.3 Alt: GAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.2 Alt: GAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08200.1 Alt: GAA| intron_variant MODIFIER(snpEff) LOC_Os07g08190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08200.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 58.556; most accessible tissue: Minghui63 flag leaf, score: 77.153 |
| vg0704183183 (J) | chr07 | 4183183 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os07g08190.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os07g08210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.3 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.2 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08200.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 59.840; most accessible tissue: Callus, score: 77.247 |
| vg0704183320 (J) | chr07 | 4183320 | T | C | 57.30% | 0.38% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g08190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.3 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08200.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 60.521; most accessible tissue: Callus, score: 77.247 |
| vg0704183416 (J) | chr07 | 4183416 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os07g08190.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.3 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.2 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08200.1 Alt: T| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 64.661; most accessible tissue: Zhenshan97 young leaf, score: 85.184 |
| vg0704183421 (J) | chr07 | 4183421 | G | A | 57.80% | 0.38% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os07g08190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.3 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08210.2 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os07g08200.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 65.039; most accessible tissue: Zhenshan97 young leaf, score: 85.364 |
| vg0704183484 (J) | chr07 | 4183484 | T | G | 99.90% | 0.00% | T -> G | NA |
LOC_Os07g08190.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os07g08210.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.3 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08210.2 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os07g08200.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.425; most accessible tissue: Zhenshan97 young leaf, score: 88.259 |
| vg0704183554 (J) | chr07 | 4183554 | T | C | 56.90% | 0.00% | C -> T | NA |
LOC_Os07g08200.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.601; most accessible tissue: Zhenshan97 young leaf, score: 89.666 |
| vg0704183556 (J) | chr07 | 4183556 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os07g08200.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 76.099; most accessible tissue: Zhenshan97 young leaf, score: 89.875 |
| vg0704183609 (J) | chr07 | 4183609 | G | A | 57.60% | 0.38% | A -> G | NA |
LOC_Os07g08200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08200.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 75.921; most accessible tissue: Minghui63 flag leaf, score: 91.558 |
| vg0704183800 (J) | chr07 | 4183800 | C | T | 99.70% | 0.00% | C -> T | NA |
LOC_Os07g08200.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 78.814; most accessible tissue: Minghui63 flag leaf, score: 92.844 |
| vg0704183911 (J) | chr07 | 4183911 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os07g08200.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 73.140; most accessible tissue: Minghui63 flag leaf, score: 92.302 |
| vg0704184047 (J) | chr07 | 4184047 | T | A | 57.30% | 0.38% | A -> T | NA |
LOC_Os07g08200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g08200.1 Alt: T| start_lost HIGH(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 73.992; most accessible tissue: Minghui63 flag leaf, score: 91.280 |