9 variations found. Os02g0785700/LOC_Os02g54450 (hypro1; putative; expressed), ranging from 33,353,939 bp to 33,355,216 bp (including 0 kb upstream and 0 kb downstream of the gene).
| Gene ID | Annotation |
|---|---|
| LOC_Os02g54450 | hypro1, putative, expressed; RAP ID: Os02g0785700; MSU ID: LOC_Os02g54450 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233354124 (J) | chr02 | 33354124 | C | CT | 91.50% | 2.41% | C -> CT | NA |
LOC_Os02g54450.1 Alt: CT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54430.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54440.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54460.1 Alt: CT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 |
| vg0233354125 (J) | chr02 | 33354125 | T | TA | 90.50% | 1.69% | T -> TA | NA |
LOC_Os02g54450.1 Alt: TA| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54430.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54440.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54460.1 Alt: TA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 59.006; most accessible tissue: Zhenshan97 flower, score: 67.236 |
| vg0233354314 (J) | chr02 | 33354314 | G | A | 98.10% | 0.00% | G -> A | NA |
LOC_Os02g54450.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.410; most accessible tissue: Minghui63 root, score: 82.185 |
| vg0233354640 (J) | chr02 | 33354640 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os02g54450.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os02g54430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54440.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54460.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54470.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54470.2 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 73.583; most accessible tissue: Zhenshan97 young leaf, score: 84.624 |
| vg0233354790 (J) | chr02 | 33354790 | G | T | 64.40% | 0.00% | T -> G | NA |
LOC_Os02g54450.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 71.413; most accessible tissue: Zhenshan97 root, score: 80.680 |
| vg0233354792 (J) | chr02 | 33354792 | G | A | 99.50% | 0.00% | G -> A | NA |
LOC_Os02g54450.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os02g54430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54440.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54460.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54470.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54470.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 71.374; most accessible tissue: Zhenshan97 root, score: 80.448 |
| vg0233354900 (J) | chr02 | 33354900 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os02g54450.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 67.361; most accessible tissue: Zhenshan97 root, score: 82.170 |
| vg0233355144 (J) | chr02 | 33355144 | A | C | 94.30% | 0.00% | A -> C |
LOC_Os02g54450.1 Alt: C| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54430.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54440.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54460.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54470.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54470.2 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 61.436; most accessible tissue: Zhenshan97 root, score: 87.558 |
|
| STR0233354126 (J) | chr02 | 33354126 | AA | AAA | 93.00% | 0.00% | AA -> AAA | NA |
|