6 variations found. Os01g0827400/LOC_Os01g61170 (prenylated rab acceptor; putative; expressed), ranging from 35,407,929 bp to 35,408,598 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os01g61170 | prenylated rab acceptor, putative; RAP ID: Os01g0827400; MSU ID: LOC_Os01g61170 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0135408113 (J) | chr01 | 35408113 | G | A | 97.40% | 0.00% | G -> A | NA |
LOC_Os01g61170.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 91.681; most accessible tissue: Zhenshan97 flag leaf, score: 96.326 |
| vg0135408199 (J) | chr01 | 35408199 | A | C | 64.50% | 0.00% | C -> A,G | NA |
LOC_Os01g61170.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os01g61180.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g61190.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g61160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g61170.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 94.426; most accessible tissue: Zhenshan97 flag leaf, score: 96.777 |
| vg0135408304 (J) | chr01 | 35408304 | A | C | 64.50% | 0.00% | C -> A | NA |
LOC_Os01g61170.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.768; most accessible tissue: Zhenshan97 flag leaf, score: 97.923 |
| vg0135408369 (J) | chr01 | 35408369 | G | T | 97.40% | 0.00% | T -> G | NA |
LOC_Os01g61170.1 Alt: G| splice_acceptor_variant&intron_variant HIGH(snpEff)/splice_acceptor_variant(CooVar)
The average chromatin accessibility score: 94.880; most accessible tissue: Zhenshan97 flag leaf, score: 98.227 |
| vg0135408468 (J) | chr01 | 35408468 | A | G | 87.10% | 0.00% | A -> G |
LOC_Os01g61170.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 98.128; most accessible tissue: Callus, score: 99.271 |
|
| STR0135408303 (J) | chr01 | 35408303 | AA | AC | 60.10% | 0.00% | AC -> AA | NA |
|