14 variations found. LOC_Os01g22620 (retrotransposon protein; putative; unclassified), ranging from 12,723,150 bp to 12,724,428 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0112723152 (J) | chr01 | 12723152 | T | C | 46.70% | 32.84% | T -> C | NA |
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g22620.1 Alt: C| stop_lost&splice_region_variant HIGH(snpEff)/stop_lost(CooVar) The average chromatin accessibility score: 16.389; most accessible tissue: Zhenshan97 flag leaf, score: 27.583 |
| vg0112723170 (J) | chr01 | 12723170 | T | C | 37.70% | 30.39% | T -> C | NA |
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g22620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 16.957; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 |
| vg0112723183 (J) | chr01 | 12723183 | C | T | 42.80% | 38.79% | C -> T | NA |
LOC_Os01g22620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.754; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 |
| vg0112723202 (J) | chr01 | 12723202 | C | G | 54.90% | 30.62% | C -> G | NA |
LOC_Os01g22620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.907; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 |
| vg0112723225 (J) | chr01 | 12723225 | C | G | 55.40% | 31.65% | C -> G | NA |
LOC_Os01g22620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.970; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 |
| vg0112723228 (J) | chr01 | 12723228 | T | C | 56.60% | 31.59% | T -> C | NA |
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g22620.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 16.970; most accessible tissue: Zhenshan97 flag leaf, score: 29.417 |
| vg0112723315 (J) | chr01 | 12723315 | G | A | 99.30% | 0.00% | G -> A | NA |
LOC_Os01g22620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 16.479; most accessible tissue: Zhenshan97 root, score: 27.411 |
| vg0112723317 (J) | chr01 | 12723317 | C | T | 99.40% | 0.00% | C -> T | NA |
LOC_Os01g22620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 16.479; most accessible tissue: Zhenshan97 root, score: 27.411 |
| vg0112723623 (J) | chr01 | 12723623 | G | A | 31.20% | 39.97% | G -> A | NA |
LOC_Os01g22620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.111; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0112723630 (J) | chr01 | 12723630 | G | A | 30.30% | 40.22% | G -> A | NA |
LOC_Os01g22620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.297; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0112723651 (J) | chr01 | 12723651 | A | G | 70.60% | 18.75% | A -> G | NA |
LOC_Os01g22620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.746; most accessible tissue: Minghui63 panicle, score: 50.413 |
| vg0112723686 (J) | chr01 | 12723686 | C | T | 62.40% | 23.83% | C -> T | NA |
LOC_Os01g22620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 20.272; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0112723740 (J) | chr01 | 12723740 | G | A | 99.40% | 0.00% | G -> A | NA |
LOC_Os01g22620.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g22630.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g22630.2 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 21.624; most accessible tissue: Minghui63 panicle, score: 46.754 |
| vg0112723984 (J) | chr01 | 12723984 | C | G | 31.70% | 41.83% | C -> G | NA |
LOC_Os01g22620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g22620.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 24.843; most accessible tissue: Zhenshan97 root, score: 43.050 |