18 variations found. Os12g0156900/LOC_Os12g06070 (expressed protein), ranging from 2,830,043 bp to 2,831,936 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os12g06070 | conserved hypothetical protein; RAP ID: Os12g0156900; MSU ID: LOC_Os12g06070 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202830210 (J) | chr12 | 2830210 | T | C | 91.60% | 0.00% | T -> C |
LOC_Os12g06070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 54.831; most accessible tissue: Callus, score: 79.554 |
|
| vg1202830223 (J) | chr12 | 2830223 | T | C | 99.90% | 0.00% | T -> C | NA |
LOC_Os12g06070.1 Alt: C| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 54.757; most accessible tissue: Callus, score: 79.554 |
| vg1202830380 (J) | chr12 | 2830380 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os12g06070.1 Alt: A| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 53.027; most accessible tissue: Zhenshan97 young leaf, score: 74.675 |
| vg1202830421 (J) | chr12 | 2830421 | T | C | 99.20% | 0.00% | T -> C | NA |
LOC_Os12g06070.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 55.158; most accessible tissue: Zhenshan97 young leaf, score: 77.422 |
| vg1202830688 (J) | chr12 | 2830688 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os12g06070.1 Alt: T| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 55.118; most accessible tissue: Callus, score: 81.656 |
| vg1202830783 (J) | chr12 | 2830783 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os12g06070.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 50.904; most accessible tissue: Callus, score: 81.656 |
| vg1202830841 (J) | chr12 | 2830841 | C | A | 95.70% | 0.00% | C -> A | NA |
LOC_Os12g06070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 46.946; most accessible tissue: Zhenshan97 young leaf, score: 67.830 |
| vg1202830847 (J) | chr12 | 2830847 | T | C | 97.30% | 0.00% | T -> C | NA |
LOC_Os12g06070.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 46.896; most accessible tissue: Zhenshan97 young leaf, score: 67.830 |
| vg1202830937 (J) | chr12 | 2830937 | T | G | 99.70% | 0.00% | T -> G | NA |
LOC_Os12g06070.1 Alt: G| synonymous_variant LOW(snpEff)
The average chromatin accessibility score: 48.925; most accessible tissue: Callus, score: 84.964 |
| vg1202830957 (J) | chr12 | 2830957 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os12g06070.1 Alt: G| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 48.175; most accessible tissue: Callus, score: 84.964 |
| vg1202830986 (J) | chr12 | 2830986 | G | A | 95.10% | 0.00% | G -> A | NA |
LOC_Os12g06070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 49.372; most accessible tissue: Callus, score: 84.964 |
| vg1202831209 (J) | chr12 | 2831209 | G | A | 98.20% | 0.00% | G -> A | NA |
LOC_Os12g06070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 49.230; most accessible tissue: Callus, score: 83.761 |
| vg1202831374 (J) | chr12 | 2831374 | G | T | 99.70% | 0.00% | G -> T | NA |
LOC_Os12g06070.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g06080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 48.888; most accessible tissue: Zhenshan97 flower, score: 69.775 |
| vg1202831485 (J) | chr12 | 2831485 | T | C | 99.70% | 0.00% | T -> C | NA |
LOC_Os12g06070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 50.892; most accessible tissue: Callus, score: 81.666 |
| vg1202831546 (J) | chr12 | 2831546 | T | C | 91.70% | 0.00% | T -> C |
LOC_Os12g06070.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 52.206; most accessible tissue: Callus, score: 81.666 |
|
| vg1202831548 (J) | chr12 | 2831548 | A | C | 99.80% | 0.00% | A -> C | NA |
LOC_Os12g06070.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os12g06080.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.065; most accessible tissue: Callus, score: 81.666 |
| vg1202831643 (J) | chr12 | 2831643 | A | T | 99.40% | 0.00% | A -> T | NA |
LOC_Os12g06070.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g06080.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 53.567; most accessible tissue: Zhenshan97 young leaf, score: 69.263 |
| vg1202831695 (J) | chr12 | 2831695 | A | C | 99.80% | 0.00% | A -> C | NA |
LOC_Os12g06070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 55.925; most accessible tissue: Callus, score: 89.063 |