13 variations found. LOC_Os01g43830 (retrotransposon protein; putative; unclassified), ranging from 25,111,721 bp to 25,112,048 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0125111738 (J) | chr01 | 25111738 | G | A | 35.70% | 42.28% | G -> A | NA |
LOC_Os01g43830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.090; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0125111745 (J) | chr01 | 25111745 | C | T | 19.10% | 68.68% | C -> T | NA |
LOC_Os01g43830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.003; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0125111760 (J) | chr01 | 25111760 | G | A | 17.60% | 77.59% | G -> A | NA |
LOC_Os01g43830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.441; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0125111763 (J) | chr01 | 25111763 | C | T | 17.60% | 73.68% | C -> T | NA |
LOC_Os01g43830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.441; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0125111765 (J) | chr01 | 25111765 | A | G | 17.60% | 75.37% | A -> G | NA |
LOC_Os01g43830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.441; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0125111832 (J) | chr01 | 25111832 | G | A | 7.50% | 77.57% | G -> A | NA |
LOC_Os01g43830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.191; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0125111853 (J) | chr01 | 25111853 | T | A | 0.50% | 96.28% | A -> T | NA |
LOC_Os01g43830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.027; most accessible tissue: Minghui63 panicle, score: 38.588 |
| vg0125111953 (J) | chr01 | 25111953 | G | T | 10.30% | 69.26% | G -> T | NA |
LOC_Os01g43830.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.920; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0125111981 (J) | chr01 | 25111981 | T | A | 47.00% | 46.78% | T -> A | NA |
LOC_Os01g43830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.906; most accessible tissue: Zhenshan97 panicle, score: 16.188 |
| vg0125111997 (J) | chr01 | 25111997 | G | A | 49.90% | 44.39% | G -> A | NA |
LOC_Os01g43830.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.081; most accessible tissue: Callus, score: 10.300 |
| vg0125112007 (J) | chr01 | 25112007 | G | A | 51.00% | 43.42% | G -> A | NA |
LOC_Os01g43830.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.081; most accessible tissue: Callus, score: 10.300 |
| vg0125112038 (J) | chr01 | 25112038 | A | G | 50.80% | 42.91% | A -> G | NA |
LOC_Os01g43830.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.081; most accessible tissue: Callus, score: 10.300 |
| vg0125112043 (J) | chr01 | 25112043 | A | G | 50.90% | 42.93% | A -> G | NA |
LOC_Os01g43830.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g43830.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.081; most accessible tissue: Callus, score: 10.300 |