11 variations found. LOC_Os06g42010 (transposon protein; putative; unclassified; expressed), ranging from 25,221,584 bp to 25,225,478 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0625222635 (J) | chr06 | 25222635 | C | T | 15.60% | 71.54% | C -> T | NA |
LOC_Os06g42010.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.838; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625222832 (J) | chr06 | 25222832 | G | A | 16.00% | 79.86% | G -> A | NA |
LOC_Os06g42010.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.781; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625222857 (J) | chr06 | 25222857 | G | A | 15.70% | 79.96% | G -> A | NA |
LOC_Os06g42010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.868; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625222860 (J) | chr06 | 25222860 | A | ACGACGC CTTGGC | 15.50% | 81.06% | A -> ACGACGCCTT GGC | NA |
LOC_Os06g42010.1 Alt: ACGACGCCTTGGC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.868; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625222861 (J) | chr06 | 25222861 | C | CG | 15.70% | 78.80% | C -> CG | NA |
LOC_Os06g42010.1 Alt: CG/frameshift_variant(CooVar)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.868; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625222862 (J) | chr06 | 25222862 | A | G | 15.60% | 78.21% | A -> G,ACGCCTTG GCCTTGC,AC GCCTTGGCCT T | NA |
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os06g42010.1 Alt: G/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) LOC_Os06g42010.1 Alt: ACGCCTTGGCCTT| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os06g42010.1 Alt: ACGCCTTGGCCTTGC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 4.868; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625222863 (J) | chr06 | 25222863 | G | A | 15.60% | 79.24% | G -> A | NA |
LOC_Os06g42010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.868; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625222953 (J) | chr06 | 25222953 | C | T | 16.40% | 68.92% | C -> T | NA |
LOC_Os06g42010.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.969; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625223164 (J) | chr06 | 25223164 | A | G | 15.60% | 78.88% | A -> G | NA |
LOC_Os06g42010.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.679; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625224357 (J) | chr06 | 25224357 | C | T | 15.30% | 72.30% | C -> T | NA |
LOC_Os06g42010.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 4.619; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625224688 (J) | chr06 | 25224688 | C | A | 15.70% | 72.39% | C -> A | NA |
LOC_Os06g42010.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g42010.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |