5 variations found. Os09g0412300/LOC_Os09g24580 (EF hand family protein; putative; expressed), ranging from 14,635,599 bp to 14,636,121 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os09g24580 | EF hand family protein, putative, expressed; RAP ID: Os09g0412300; MSU ID: LOC_Os09g24580 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0914635605 (J) | chr09 | 14635605 | C | T | 95.90% | 0.00% | C -> T | NA |
LOC_Os09g24580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 88.612; most accessible tissue: Minghui63 flag leaf, score: 98.955 |
| vg0914635669 (J) | chr09 | 14635669 | G | A | 98.30% | 0.00% | G -> A | NA |
LOC_Os09g24580.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.317; most accessible tissue: Minghui63 flag leaf, score: 99.282 |
| vg0914635830 (J) | chr09 | 14635830 | C | A | 90.50% | 0.00% | A -> C | NA |
LOC_Os09g24580.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os09g24570.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 91.770; most accessible tissue: Minghui63 flag leaf, score: 99.528 |
| vg0914635883 (J) | chr09 | 14635883 | G | A | 99.00% | 0.00% | G -> A | NA |
LOC_Os09g24580.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 92.426; most accessible tissue: Minghui63 flag leaf, score: 99.607 |
| vg0914636102 (J) | chr09 | 14636102 | G | T | 93.70% | 0.00% | G -> T | NA |
LOC_Os09g24580.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 97.779; most accessible tissue: Minghui63 flag leaf, score: 99.849 |