9 variations found. LOC_Os06g13500 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 7,439,411 bp to 7,443,218 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0607439497 (J) | chr06 | 7439497 | C | T | 2.90% | 94.56% | C -> T | NA |
LOC_Os06g13500.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.961; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0607439503 (J) | chr06 | 7439503 | G | A | 2.60% | 94.94% | G -> A | NA |
LOC_Os06g13500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.961; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0607439520 (J) | chr06 | 7439520 | T | A | 0.70% | 95.56% | T -> A | NA |
LOC_Os06g13500.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 9.154; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg0607439898 (J) | chr06 | 7439898 | G | A | 0.40% | 97.38% | A -> G | NA |
LOC_Os06g13500.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 8.897; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0607440885 (J) | chr06 | 7440885 | T | C | 28.50% | 61.47% | T -> C | NA |
LOC_Os06g13500.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0607440891 (J) | chr06 | 7440891 | G | C | 28.50% | 61.40% | G -> C,A | NA |
LOC_Os06g13500.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g13500.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0607440894 (J) | chr06 | 7440894 | T | A | 28.60% | 61.36% | T -> A,G | NA |
LOC_Os06g13500.1 Alt: G| synonymous_variant LOW(snpEff)
LOC_Os06g13500.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0607440921 (J) | chr06 | 7440921 | A | T | 8.30% | 81.49% | A -> T | NA |
LOC_Os06g13500.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |
| vg0607440927 (J) | chr06 | 7440927 | T | G | 6.50% | 86.56% | T -> G | NA |
LOC_Os06g13500.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g13500.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976 |