5 variations found. Os11g0242900/LOC_Os11g13900 (expressed protein), ranging from 7,678,685 bp to 7,679,890 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os11g13900 | hypothetical protein; RAP ID: Os11g0242900; MSU ID: LOC_Os11g13900 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1107678718 (J) | chr11 | 7678718 | G | A | 41.80% | 49.79% | G -> A | NA |
LOC_Os11g13900.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g13900.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.775; most accessible tissue: Callus, score: 18.856 |
| vg1107678757 (J) | chr11 | 7678757 | G | A | 41.60% | 50.85% | G -> A | NA |
LOC_Os11g13900.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g13900.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.775; most accessible tissue: Callus, score: 18.856 |
| vg1107679366 (J) | chr11 | 7679366 | C | T | 41.80% | 51.48% | C -> T | NA |
LOC_Os11g13910.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g13920.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g13900.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.932; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1107679379 (J) | chr11 | 7679379 | G | A | 41.80% | 51.21% | G -> A | NA |
LOC_Os11g13910.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g13920.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g13900.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.932; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1107679454 (J) | chr11 | 7679454 | G | A | 39.40% | 51.88% | G -> A | NA |
LOC_Os11g13900.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g13900.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.940; most accessible tissue: Minghui63 panicle, score: 7.125 |