9 variations found. LOC_Os06g16230 (transposon protein; putative; unclassified; expressed), ranging from 9,237,952 bp to 9,244,110 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0609240321 (J) | chr06 | 9240321 | T | A | 13.10% | 82.46% | T -> A | NA |
LOC_Os06g16230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609240670 (J) | chr06 | 9240670 | A | G | 12.70% | 82.84% | A -> G | NA |
LOC_Os06g16230.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609241987 (J) | chr06 | 9241987 | T | C | 12.40% | 84.02% | T -> C | NA |
LOC_Os06g16230.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609242032 (J) | chr06 | 9242032 | G | A | 12.40% | 83.90% | G -> A | NA |
LOC_Os06g16230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609242047 (J) | chr06 | 9242047 | C | A | 12.40% | 83.86% | C -> A | NA |
LOC_Os06g16230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609242368 (J) | chr06 | 9242368 | G | A | 12.40% | 84.38% | G -> A | NA |
LOC_Os06g16230.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609242768 (J) | chr06 | 9242768 | C | T | 3.00% | 89.12% | C -> T | NA |
LOC_Os06g16230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.372; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609243656 (J) | chr06 | 9243656 | G | A | 3.90% | 88.79% | G -> A | NA |
LOC_Os06g16230.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.364; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0609244062 (J) | chr06 | 9244062 | C | T | 12.50% | 84.43% | C -> T | NA |
LOC_Os06g16230.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os06g16230.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |