17 variations found. LOC_Os12g27800 (retrotransposon protein; putative; unclassified; expressed), ranging from 16,386,801 bp to 16,389,456 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1216386902 (J) | chr12 | 16386902 | G | A | 98.70% | 0.55% | G -> A | NA |
LOC_Os12g27800.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g27810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g27790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 11.011; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg1216386926 (J) | chr12 | 16386926 | G | A | 98.90% | 0.55% | G -> A | NA |
LOC_Os12g27800.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g27810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g27790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 11.643; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg1216386930 (J) | chr12 | 16386930 | C | T | 94.00% | 0.72% | C -> T | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 11.643; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg1216386947 (J) | chr12 | 16386947 | C | T | 98.80% | 0.68% | C -> T | NA |
LOC_Os12g27800.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g27810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os12g27790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 11.730; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg1216387128 (J) | chr12 | 16387128 | G | A | 19.40% | 74.21% | G -> A | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 9.491; most accessible tissue: Minghui63 panicle, score: 16.270 |
| vg1216387240 (J) | chr12 | 16387240 | G | A | 54.80% | 18.47% | G -> A | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.247; most accessible tissue: Callus, score: 10.072 |
| vg1216387261 (J) | chr12 | 16387261 | C | A | 73.00% | 11.26% | C -> A | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.247; most accessible tissue: Callus, score: 10.072 |
| vg1216387273 (J) | chr12 | 16387273 | T | C | 74.50% | 10.73% | T -> C | NA |
LOC_Os12g27800.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g27800.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.247; most accessible tissue: Callus, score: 10.072 |
| vg1216387274 (J) | chr12 | 16387274 | G | A | 74.70% | 10.69% | G -> A | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.247; most accessible tissue: Callus, score: 10.072 |
| vg1216387285 (J) | chr12 | 16387285 | G | A | 74.00% | 10.66% | G -> A | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 5.247; most accessible tissue: Callus, score: 10.072 |
| vg1216387308 (J) | chr12 | 16387308 | T | C | 74.50% | 10.64% | T -> C | NA |
LOC_Os12g27800.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.247; most accessible tissue: Callus, score: 10.072 |
| vg1216387320 (J) | chr12 | 16387320 | G | A | 68.30% | 12.27% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g27800.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g27810.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g27790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 5.159; most accessible tissue: Callus, score: 10.072 |
| vg1216387327 (J) | chr12 | 16387327 | A | AT | 27.50% | 61.32% | A -> AT | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g27810.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g27790.1 Alt: AT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g27800.1 Alt: AT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.716; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1216387330 (J) | chr12 | 16387330 | A | T | 22.60% | 73.85% | A -> T | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g27810.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g27790.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g27800.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 4.716; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1216387459 (J) | chr12 | 16387459 | G | A | 21.80% | 75.73% | G -> A | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 4.533; most accessible tissue: Minghui63 panicle, score: 7.125 |
| vg1216389415 (J) | chr12 | 16389415 | T | C | 19.30% | 74.35% | T -> C | NA |
LOC_Os12g27800.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g27800.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.078; most accessible tissue: Zhenshan97 flower, score: 9.663 |
| vg1216389416 (J) | chr12 | 16389416 | G | A | 19.60% | 74.99% | G -> A | NA |
LOC_Os12g27800.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g27800.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 5.078; most accessible tissue: Zhenshan97 flower, score: 9.663 |