11 variations found. LOC_Os06g42500 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 25,551,259 bp to 25,554,960 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0625552984 (J) | chr06 | 25552984 | C | A | 12.70% | 82.71% | C -> A | NA |
LOC_Os06g42500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 7.911; most accessible tissue: Zhenshan97 flower, score: 13.891 |
| vg0625553363 (J) | chr06 | 25553363 | G | A | 12.80% | 83.39% | G -> A | NA |
LOC_Os06g42500.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.500; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625553635 (J) | chr06 | 25553635 | G | A | 13.90% | 79.33% | G -> A | NA |
LOC_Os06g42500.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.435; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0625554229 (J) | chr06 | 25554229 | C | T | 0.70% | 84.74% | C -> T | NA |
LOC_Os06g42500.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0625554505 (J) | chr06 | 25554505 | C | T | 6.50% | 74.74% | C -> T | NA |
LOC_Os06g42500.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 12.936; most accessible tissue: Zhenshan97 root, score: 18.731 |
| vg0625554535 (J) | chr06 | 25554535 | G | T | 7.00% | 71.65% | G -> T | NA |
LOC_Os06g42500.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.143; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg0625554578 (J) | chr06 | 25554578 | G | A | 70.00% | 24.12% | G -> A | NA |
LOC_Os06g42500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 15.590; most accessible tissue: Minghui63 young leaf, score: 22.423 |
| vg0625554606 (J) | chr06 | 25554606 | C | T | 65.00% | 24.23% | C -> T | NA |
LOC_Os06g42500.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.050; most accessible tissue: Minghui63 young leaf, score: 24.836 |
| vg0625554647 (J) | chr06 | 25554647 | G | A | 69.70% | 23.99% | G -> A | NA |
LOC_Os06g42500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.339; most accessible tissue: Minghui63 young leaf, score: 26.082 |
| vg0625554658 (J) | chr06 | 25554658 | A | C | 46.20% | 35.65% | A -> C | NA |
LOC_Os06g42500.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 16.339; most accessible tissue: Minghui63 young leaf, score: 26.082 |
| vg0625554937 (J) | chr06 | 25554937 | T | C | 2.70% | 67.52% | C -> T | NA |
LOC_Os06g42500.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g42500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.857; most accessible tissue: Minghui63 root, score: 15.664 |