8 variations found. LOC_Os02g54530 (SCP-like extracellular protein; expressed), ranging from 33,405,034 bp to 33,405,605 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0233405038 (J) | chr02 | 33405038 | GA | G | 62.20% | 0.00% | G -> GA,A | NA |
LOC_Os02g54530.1 Alt: A| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g54540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54520.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54530.1 Alt: GA| 5_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54540.1 Alt: GA| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os02g54520.1 Alt: GA| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 89.096; most accessible tissue: Zhenshan97 panicle, score: 97.661 |
| vg0233405111 (J) | chr02 | 33405111 | C | A | 62.40% | 0.00% | A -> C | NA |
LOC_Os02g54530.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.020; most accessible tissue: Zhenshan97 panicle, score: 98.362 |
| vg0233405134 (J) | chr02 | 33405134 | T | C | 62.30% | 0.00% | C -> T | NA |
LOC_Os02g54530.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.341; most accessible tissue: Zhenshan97 panicle, score: 98.621 |
| vg0233405142 (J) | chr02 | 33405142 | AGTC | A | 99.90% | 0.00% | AGTC -> A | NA |
LOC_Os02g54530.1 Alt: A| inframe_deletion MODERATE(snpEff)
LOC_Os02g54540.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os02g54520.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 86.822; most accessible tissue: Zhenshan97 panicle, score: 98.602 |
| vg0233405212 (J) | chr02 | 33405212 | G | C | 94.30% | 0.00% | G -> C |
LOC_Os02g54530.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 88.888; most accessible tissue: Zhenshan97 panicle, score: 98.842 |
|
| vg0233405315 (J) | chr02 | 33405315 | G | T | 26.70% | 16.80% | G -> T | NA |
LOC_Os02g54530.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g54530.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 89.213; most accessible tissue: Zhenshan97 panicle, score: 98.901 |
| vg0233405451 (J) | chr02 | 33405451 | C | G | 51.10% | 15.83% | G -> C | NA |
LOC_Os02g54530.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g54530.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 89.699; most accessible tissue: Zhenshan97 panicle, score: 99.225 |
| STR0233405039 (J) | chr02 | 33405039 | AA | A | 63.20% | 0.00% | A -> AA | NA |
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