17 variations found. LOC_Os12g35970 (transposon protein; putative; CACTA; En%2FSpm sub-class), ranging from 21,988,159 bp to 21,992,530 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1221989802 (J) | chr12 | 21989802 | C | T | 66.80% | 29.33% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g35970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.282; most accessible tissue: Minghui63 root, score: 17.665 |
| vg1221989962 (J) | chr12 | 21989962 | C | T | 66.80% | 29.12% | C -> T | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 10.624; most accessible tissue: Minghui63 flag leaf, score: 17.373 |
| vg1221990006 (J) | chr12 | 21990006 | G | T | 66.80% | 29.90% | G -> T | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: T/stop_gained(CooVar) The average chromatin accessibility score: 10.314; most accessible tissue: Minghui63 flag leaf, score: 17.021 |
| vg1221990008 (J) | chr12 | 21990008 | G | A | 66.80% | 30.00% | G -> A | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: A| synonymous_variant LOW(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 10.505; most accessible tissue: Minghui63 flag leaf, score: 17.021 |
| vg1221990052 (J) | chr12 | 21990052 | C | T | 31.10% | 30.30% | C -> T | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 11.224; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg1221990092 (J) | chr12 | 21990092 | T | C | 66.40% | 29.52% | T -> C | NA |
LOC_Os12g35970.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 11.888; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg1221990146 (J) | chr12 | 21990146 | C | T | 66.30% | 30.34% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g35980.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g35970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 11.452; most accessible tissue: Minghui63 panicle, score: 25.313 |
| vg1221990382 (J) | chr12 | 21990382 | G | A | 65.90% | 22.60% | G -> A | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 19.176; most accessible tissue: Minghui63 young leaf, score: 51.901 |
| vg1221990390 (J) | chr12 | 21990390 | C | T | 65.90% | 22.81% | C -> T | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 19.247; most accessible tissue: Minghui63 young leaf, score: 51.901 |
| vg1221990395 (J) | chr12 | 21990395 | T | A | 72.00% | 16.69% | T -> A | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 19.621; most accessible tissue: Minghui63 young leaf, score: 51.901 |
| vg1221990654 (J) | chr12 | 21990654 | C | T | 66.10% | 30.72% | C -> T | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 15.948; most accessible tissue: Minghui63 young leaf, score: 40.718 |
| vg1221990689 (J) | chr12 | 21990689 | C | T | 66.20% | 30.64% | C -> T | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 13.708; most accessible tissue: Minghui63 young leaf, score: 29.964 |
| vg1221990747 (J) | chr12 | 21990747 | C | G | 65.10% | 26.58% | C -> G | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 13.563; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg1221991387 (J) | chr12 | 21991387 | G | A | 64.10% | 30.68% | G -> A | NA |
LOC_Os12g35970.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g35970.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.953; most accessible tissue: Minghui63 flower, score: 13.501 |
| vg1221991830 (J) | chr12 | 21991830 | G | A | 66.50% | 30.64% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g35980.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g35970.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 10.414; most accessible tissue: Minghui63 flower, score: 20.805 |
| vg1221991935 (J) | chr12 | 21991935 | T | C | 58.50% | 35.00% | T -> C | NA |
LOC_Os12g35980.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g35970.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.404; most accessible tissue: Minghui63 flower, score: 21.533 |
| vg1221992283 (J) | chr12 | 21992283 | C | T | 65.00% | 31.19% | C -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g35980.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g35970.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.928; most accessible tissue: Minghui63 flower, score: 12.456 |