8 variations found. LOC_Os04g16700 (retrotransposon protein; putative; Ty3-gypsy subclass), ranging from 9,085,063 bp to 9,086,420 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0409085091 (J) | chr04 | 9085091 | ACG | A | 20.40% | 72.39% | ACG -> A,AGATAGAT CTAGCG | NA |
LOC_Os04g16700.1 Alt: AGATAGATCTAGCG| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os04g16700.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os04g16700.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 15.975; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0409085094 (J) | chr04 | 9085094 | G | GAT | 20.40% | 73.19% | G -> GAT | NA |
LOC_Os04g16700.1 Alt: GAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os04g16700.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.975; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0409085097 (J) | chr04 | 9085097 | C | A | 20.40% | 73.49% | C -> A | NA |
LOC_Os04g16700.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g16700.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 15.787; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0409085829 (J) | chr04 | 9085829 | G | C | 20.40% | 77.72% | G -> C | NA |
LOC_Os04g16690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os04g16710.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16712.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16700.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.400; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0409086123 (J) | chr04 | 9086123 | C | A | 21.00% | 78.18% | C -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g16690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16710.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16712.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16700.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0409086131 (J) | chr04 | 9086131 | A | T | 21.00% | 76.51% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g16690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16712.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0409086204 (J) | chr04 | 9086204 | A | G | 21.10% | 76.64% | A -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g16690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16710.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16712.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16700.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0409086207 (J) | chr04 | 9086207 | G | T | 21.10% | 76.72% | G -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os04g16690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16710.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16712.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os04g16700.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |