5 variations found. LOC_Os04g44570 (aquaporin protein; putative; expressed), ranging from 26,380,264 bp to 26,381,607 bp (including 0 kb upstream and 0 kb downstream of the gene).
| 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0426380288 (J) | chr04 | 26380288 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os04g44570.1 Alt: G| 5_prime_UTR_variant MODIFIER(snpEff)
LOC_Os04g44560.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os04g44580.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 91.344; most accessible tissue: Callus, score: 99.106 |
| vg0426380557 (J) | chr04 | 26380557 | AT | A | 98.40% | 0.00% | AT -> A,ATT | NA |
LOC_Os04g44560.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44580.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44570.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44560.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44580.1 Alt: ATT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44570.1 Alt: ATT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.582; most accessible tissue: Callus, score: 94.179 |
| vg0426380700 (J) | chr04 | 26380700 | C | T | 98.80% | 0.00% | C -> T | NA |
LOC_Os04g44570.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 89.796; most accessible tissue: Minghui63 panicle, score: 93.837 |
| vg0426380865 (J) | chr04 | 26380865 | G | A | 98.80% | 0.00% | G -> A | NA |
LOC_Os04g44560.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g44580.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g44570.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 87.539; most accessible tissue: Minghui63 panicle, score: 93.294 |
| vg0426381252 (J) | chr04 | 26381252 | G | C | 98.60% | 0.00% | G -> C | NA |
LOC_Os04g44570.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 88.109; most accessible tissue: Callus, score: 93.423 |