17 variations found. LOC_Os07g36710 (retrotransposon protein; putative; unclassified; expressed), ranging from 21,993,410 bp to 21,995,822 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0721993420 (J) | chr07 | 21993420 | G | A | 96.40% | 2.41% | G -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 31.447; most accessible tissue: Minghui63 root, score: 61.650 |
| vg0721993438 (J) | chr07 | 21993438 | G | A | 92.50% | 2.39% | G -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 25.719; most accessible tissue: Minghui63 root, score: 49.234 |
| vg0721993450 (J) | chr07 | 21993450 | A | G | 95.70% | 0.51% | A -> G | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 24.765; most accessible tissue: Minghui63 root, score: 47.894 |
| vg0721993454 (J) | chr07 | 21993454 | G | A | 95.10% | 1.63% | G -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 24.584; most accessible tissue: Minghui63 root, score: 47.894 |
| vg0721993465 (J) | chr07 | 21993465 | C | Unkown | 97.10% | 1.63% | C -> T | NA |
LOC_Os07g36710.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os07g36720.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g36700.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 20.497; most accessible tissue: Minghui63 root, score: 38.567 |
| vg0721993474 (J) | chr07 | 21993474 | AC | A | 90.90% | 1.76% | AC -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 17.826; most accessible tissue: Callus, score: 32.482 |
| vg0721993476 (J) | chr07 | 21993476 | C | T | 95.80% | 1.63% | C -> T | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 17.378; most accessible tissue: Callus, score: 32.482 |
| vg0721993506 (J) | chr07 | 21993506 | G | A | 88.00% | 8.65% | G -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 7.197; most accessible tissue: Callus, score: 32.482 |
| vg0721993517 (J) | chr07 | 21993517 | T | A | 59.00% | 21.33% | T -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 7.589; most accessible tissue: Callus, score: 32.482 |
| vg0721993610 (J) | chr07 | 21993610 | G | A | 34.90% | 30.70% | G -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 9.702; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg0721993779 (J) | chr07 | 21993779 | G | A | 97.00% | 1.67% | G -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 11.981; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg0721993814 (J) | chr07 | 21993814 | A | Unkown | 97.60% | 1.63% | A -> T | NA |
LOC_Os07g36710.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os07g36720.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os07g36700.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 11.981; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg0721993869 (J) | chr07 | 21993869 | C | A | 89.80% | 2.69% | C -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 12.163; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg0721994365 (J) | chr07 | 21994365 | C | G | 79.30% | 12.21% | C -> G | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.565; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg0721994987 (J) | chr07 | 21994987 | G | C | 15.50% | 33.52% | G -> C | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 5.506; most accessible tissue: Callus, score: 15.897 |
| vg0721995082 (J) | chr07 | 21995082 | T | C | 35.80% | 30.24% | T -> C | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.426; most accessible tissue: Callus, score: 15.021 |
| vg0721995140 (J) | chr07 | 21995140 | G | A | 76.20% | 9.14% | G -> A | NA |
LOC_Os07g36710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os07g36710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.426; most accessible tissue: Callus, score: 15.021 |