9 variations found. LOC_Os08g36530 (aspartic proteinase nepenthesin precursor; putative; expressed), ranging from 23,065,633 bp to 23,066,980 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0823065762 (J) | chr08 | 23065762 | G | A | 97.50% | 0.00% | G -> A | NA |
LOC_Os08g36530.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.101; most accessible tissue: Zhenshan97 root, score: 90.081 |
| vg0823065830 (J) | chr08 | 23065830 | C | A | 97.40% | 0.00% | C -> A | NA |
LOC_Os08g36530.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 81.598; most accessible tissue: Zhenshan97 panicle, score: 89.846 |
| vg0823066065 (J) | chr08 | 23066065 | C | G | 97.50% | 0.00% | C -> G | NA |
LOC_Os08g36530.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 84.230; most accessible tissue: Zhenshan97 young leaf, score: 91.689 |
| vg0823066082 (J) | chr08 | 23066082 | C | T | 97.50% | 0.00% | C -> T | NA |
LOC_Os08g36530.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.498; most accessible tissue: Zhenshan97 young leaf, score: 91.542 |
| vg0823066083 (J) | chr08 | 23066083 | G | T | 97.50% | 0.00% | G -> T | NA |
LOC_Os08g36530.1 Alt: T| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 82.220; most accessible tissue: Zhenshan97 young leaf, score: 91.311 |
| vg0823066107 (J) | chr08 | 23066107 | G | T | 66.60% | 0.13% | T -> G | NA |
LOC_Os08g36530.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g36530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 82.118; most accessible tissue: Zhenshan97 young leaf, score: 91.151 |
| vg0823066434 (J) | chr08 | 23066434 | A | C | 97.50% | 0.00% | A -> C | NA |
LOC_Os08g36530.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 72.431; most accessible tissue: Zhenshan97 flower, score: 81.325 |
| vg0823066655 (J) | chr08 | 23066655 | A | G | 53.30% | 0.25% | G -> A | NA |
LOC_Os08g36530.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g36530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 68.765; most accessible tissue: Zhenshan97 flower, score: 81.460 |
| vg0823066777 (J) | chr08 | 23066777 | C | T | 99.90% | 0.00% | C -> T | NA |
LOC_Os08g36530.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os08g36520.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os08g36540.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 72.400; most accessible tissue: Minghui63 root, score: 82.511 |