19 variations found. LOC_Os06g14150 (retrotransposon protein; putative; unclassified; expressed), ranging from 7,892,437 bp to 7,895,856 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0607892740 (J) | chr06 | 7892740 | G | A | 6.70% | 90.75% | G -> A | NA |
LOC_Os06g14150.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g14150.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0607893717 (J) | chr06 | 7893717 | C | T | 7.00% | 91.62% | C -> T | NA |
LOC_Os06g14140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893720 (J) | chr06 | 7893720 | G | A | 7.00% | 91.43% | G -> A | NA |
LOC_Os06g14140.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893722 (J) | chr06 | 7893722 | C | T | 7.10% | 91.43% | C -> T | NA |
LOC_Os06g14140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893738 (J) | chr06 | 7893738 | A | G | 7.00% | 90.82% | A -> G | NA |
LOC_Os06g14140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893739 (J) | chr06 | 7893739 | A | G | 12.70% | 74.44% | A -> G | NA |
LOC_Os06g14140.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893742 (J) | chr06 | 7893742 | C | T | 16.30% | 69.40% | C -> T | NA |
LOC_Os06g14140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893756 (J) | chr06 | 7893756 | C | T | 7.00% | 90.88% | C -> T | NA |
LOC_Os06g14140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893778 (J) | chr06 | 7893778 | C | T | 7.80% | 90.73% | C -> T | NA |
LOC_Os06g14140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893783 (J) | chr06 | 7893783 | C | T | 8.10% | 86.29% | C -> T | NA |
LOC_Os06g14140.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os06g14160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893786 (J) | chr06 | 7893786 | T | C | 6.90% | 90.99% | T -> C,TC | NA |
LOC_Os06g14150.1 Alt: TC| splice_region_variant&intron_variant LOW(snpEff)
LOC_Os06g14140.1 Alt: TC| upstream_gene_variant MODIFIER(snpEff) LOC_Os06g14160.1 Alt: TC| downstream_gene_variant MODIFIER(snpEff) N Alt: DEL/silent_mutation(CooVar) LOC_Os06g14140.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14150.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893790 (J) | chr06 | 7893790 | T | C | 8.90% | 82.46% | T -> C | NA |
LOC_Os06g14150.1 Alt: C| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar)
LOC_Os06g14140.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os06g14160.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893794 (J) | chr06 | 7893794 | G | A | 8.30% | 89.17% | G -> A | NA |
LOC_Os06g14150.1 Alt: A| splice_acceptor_variant&intron_variant HIGH(snpEff)/splice_acceptor_variant(CooVar)
LOC_Os06g14150.1 Alt: DEL/splice_acceptor_variant(CooVar) The average chromatin accessibility score: 6.831; most accessible tissue: Callus, score: 21.877 |
| vg0607893822 (J) | chr06 | 7893822 | T | G | 7.00% | 90.96% | T -> G | NA |
LOC_Os06g14150.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os06g14150.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.421; most accessible tissue: Callus, score: 21.877 |
| vg0607893841 (J) | chr06 | 7893841 | G | A | 6.60% | 92.26% | G -> A | NA |
LOC_Os06g14150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g14150.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.489; most accessible tissue: Callus, score: 21.670 |
| vg0607894551 (J) | chr06 | 7894551 | G | A | 8.40% | 87.13% | G -> A | NA |
LOC_Os06g14150.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g14150.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.634; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg0607895058 (J) | chr06 | 7895058 | G | A | 0.50% | 94.37% | G -> A | NA |
LOC_Os06g14150.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g14150.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.300; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0607895093 (J) | chr06 | 7895093 | G | A | 0.50% | 94.03% | G -> A | NA |
LOC_Os06g14150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g14150.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.819; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0607895107 (J) | chr06 | 7895107 | A | G | 0.40% | 94.10% | G -> A | NA |
LOC_Os06g14150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os06g14150.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.819; most accessible tissue: Zhenshan97 panicle, score: 16.188 |