19 variations found. LOC_Os01g15070 (retrotransposon protein; putative; unclassified), ranging from 8,457,425 bp to 8,457,686 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0108457464 (J) | chr01 | 8457464 | T | C | 92.80% | 0.00% | T -> C | NA |
LOC_Os01g15070.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 56.247; most accessible tissue: Minghui63 young leaf, score: 70.655 |
| vg0108457498 (J) | chr01 | 8457498 | CAA | C | 92.80% | 0.00% | CAA -> C | NA |
LOC_Os01g15070.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 57.830; most accessible tissue: Minghui63 young leaf, score: 70.655 |
| vg0108457524 (J) | chr01 | 8457524 | G | C | 92.70% | 0.00% | G -> C,T | NA |
LOC_Os01g15070.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g15080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g15070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 58.973; most accessible tissue: Minghui63 young leaf, score: 71.254 |
| vg0108457571 (J) | chr01 | 8457571 | G | Unkown | 85.30% | 12.19% | G -> A | NA |
LOC_Os01g15070.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g15080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 58.037; most accessible tissue: Zhenshan97 root, score: 69.506 |
| vg0108457578 (J) | chr01 | 8457578 | C | Unkown | 85.30% | 12.19% | C -> T | NA |
LOC_Os01g15070.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g15080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.391; most accessible tissue: Zhenshan97 root, score: 69.506 |
| vg0108457584 (J) | chr01 | 8457584 | C | Unkown | 98.90% | 0.51% | C -> T | NA |
LOC_Os01g15070.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os01g15080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.664; most accessible tissue: Zhenshan97 root, score: 68.908 |
| vg0108457594 (J) | chr01 | 8457594 | G | Unkown | 73.60% | 23.02% | G -> A,T | NA |
LOC_Os01g15070.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g15080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os01g15070.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os01g15080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 55.996; most accessible tissue: Minghui63 young leaf, score: 70.038 |
| vg0108457600 (J) | chr01 | 8457600 | G | A | 93.50% | 0.13% | G -> A | NA |
LOC_Os01g15070.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g15070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 54.868; most accessible tissue: Minghui63 young leaf, score: 69.400 |
| vg0108457605 (J) | chr01 | 8457605 | G | A | 99.90% | 0.00% | G -> A | NA |
LOC_Os01g15070.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os01g15080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 54.262; most accessible tissue: Minghui63 young leaf, score: 68.745 |
| vg0108457609 (J) | chr01 | 8457609 | A | G | 43.30% | 31.80% | A -> G | NA |
LOC_Os01g15070.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g15070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 53.642; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0108457613 (J) | chr01 | 8457613 | T | C | 75.70% | 18.92% | T -> C | NA |
LOC_Os01g15070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g15070.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 53.082; most accessible tissue: Zhenshan97 panicle, score: 67.020 |
| vg0108457619 (J) | chr01 | 8457619 | A | Unkown | 85.90% | 6.81% | A -> T | NA |
LOC_Os01g15070.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g15080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.432; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0108457621 (J) | chr01 | 8457621 | G | T | 99.80% | 0.00% | G -> T | NA |
LOC_Os01g15070.1 Alt: T| stop_gained HIGH(snpEff)
LOC_Os01g15080.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.322; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0108457625 (J) | chr01 | 8457625 | A | G | 99.90% | 0.00% | A -> G | NA |
LOC_Os01g15070.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os01g15080.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: G| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 51.416; most accessible tissue: Zhenshan97 panicle, score: 68.538 |
| vg0108457638 (J) | chr01 | 8457638 | C | CA | 93.10% | 0.02% | C -> CA | NA |
LOC_Os01g15070.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g15070.1 Alt: CA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 52.341; most accessible tissue: Zhenshan97 panicle, score: 69.946 |
| vg0108457639 (J) | chr01 | 8457639 | G | Unkown | 94.20% | 0.57% | G -> A | NA |
LOC_Os01g15070.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g15080.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15090.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g15060.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 52.565; most accessible tissue: Zhenshan97 panicle, score: 69.946 |
| vg0108457644 (J) | chr01 | 8457644 | C | T | 97.80% | 0.59% | C -> T | NA |
LOC_Os01g15070.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g15070.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 53.831; most accessible tissue: Zhenshan97 panicle, score: 72.468 |
| vg0108457671 (J) | chr01 | 8457671 | C | G | 92.60% | 0.00% | C -> G,A | NA |
LOC_Os01g15070.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g15070.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 57.238; most accessible tissue: Zhenshan97 panicle, score: 75.670 |
| vg0108457673 (J) | chr01 | 8457673 | C | T | 92.90% | 0.00% | C -> T | NA |
LOC_Os01g15070.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 57.517; most accessible tissue: Zhenshan97 panicle, score: 75.670 |