54 variations found. LOC_Os12g30780 (retrotransposon protein; putative; unclassified; expressed), ranging from 18,480,206 bp to 18,481,536 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1218480219 (J) | chr12 | 18480219 | T | C | 13.10% | 74.57% | T -> C |
LOC_Os12g30780.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os12g30780.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar) LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.282; most accessible tissue: Callus, score: 21.903 |
|
| vg1218480220 (J) | chr12 | 18480220 | G | A | 16.80% | 72.45% | G -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 10.282; most accessible tissue: Callus, score: 21.903 |
| vg1218480248 (J) | chr12 | 18480248 | C | T | 30.00% | 64.33% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 10.390; most accessible tissue: Callus, score: 21.903 |
| vg1218480317 (J) | chr12 | 18480317 | G | A | 13.30% | 84.49% | G -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 8.523; most accessible tissue: Callus, score: 21.903 |
| vg1218480372 (J) | chr12 | 18480372 | G | A | 31.20% | 52.35% | G -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.164; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480412 (J) | chr12 | 18480412 | G | A | 37.20% | 50.02% | G -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 6.918; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480424 (J) | chr12 | 18480424 | C | T | 36.70% | 49.94% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 6.828; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480449 (J) | chr12 | 18480449 | C | T | 21.30% | 56.71% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 6.758; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480505 (J) | chr12 | 18480505 | C | T | 19.80% | 72.81% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 6.758; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480537 (J) | chr12 | 18480537 | G | A | 16.10% | 72.05% | G -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480538 (J) | chr12 | 18480538 | T | A | 13.00% | 77.57% | T -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480563 (J) | chr12 | 18480563 | G | T | 22.20% | 66.63% | G -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480566 (J) | chr12 | 18480566 | G | A | 31.60% | 62.95% | G -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 6.845; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480603 (J) | chr12 | 18480603 | G | A | 33.80% | 61.38% | G -> A | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.277; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480608 (J) | chr12 | 18480608 | C | T | 31.10% | 63.46% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 6.277; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480619 (J) | chr12 | 18480619 | A | G | 29.90% | 62.63% | A -> G | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 6.277; most accessible tissue: Minghui63 young leaf, score: 11.521 |
| vg1218480675 (J) | chr12 | 18480675 | C | T | 13.20% | 81.93% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 7.299; most accessible tissue: Callus, score: 17.876 |
| vg1218480729 (J) | chr12 | 18480729 | C | T | 37.80% | 49.24% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 6.845; most accessible tissue: Callus, score: 17.876 |
| vg1218480780 (J) | chr12 | 18480780 | C | T | 33.70% | 52.58% | C -> T | NA |
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g30780.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 6.619; most accessible tissue: Callus, score: 17.876 |
| vg1218480799 (J) | chr12 | 18480799 | T | C | 13.80% | 80.32% | T -> C | NA |
LOC_Os12g30780.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os12g30780.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.619; most accessible tissue: Callus, score: 17.876 |
| vg1218480868 (J) | chr12 | 18480868 | G | A | 13.30% | 82.35% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30780.1 Alt: A| splice_region_variant&intron_variant LOW(snpEff)/silent_mutation(CooVar) LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 6.762; most accessible tissue: Callus, score: 17.698 |
| vg1218480894 (J) | chr12 | 18480894 | A | C | 12.90% | 83.45% | A -> C | NA |
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 8.410; most accessible tissue: Callus, score: 17.698 |
| vg1218480907 (J) | chr12 | 18480907 | T | C | 12.80% | 86.16% | T -> C | NA |
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.786; most accessible tissue: Minghui63 panicle, score: 20.733 |
| vg1218480937 (J) | chr12 | 18480937 | G | A | 18.60% | 69.11% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os12g30770.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g30790.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g30780.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 13.265; most accessible tissue: Minghui63 panicle, score: 29.741 |
| vg1218480994 (J) | chr12 | 18480994 | T | C | 12.80% | 85.15% | T -> C | NA |
LOC_Os12g30770.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os12g30790.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os12g30780.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 25.323; most accessible tissue: Minghui63 panicle, score: 42.799 |
Address: Room B111, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural university, Wuhan, 430070, China
Comments or Questions? Please contact us. Our website: http://xielab.ncpgr.cn/