27 variations found. LOC_Os12g37680 (hypothetical protein), ranging from 23,130,845 bp to 23,131,103 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1223130849 (J) | chr12 | 23130849 | AC | A | 97.50% | 1.52% | AC -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 87.035; most accessible tissue: Minghui63 flag leaf, score: 99.571 |
| vg1223130850 (J) | chr12 | 23130850 | CA | C | 43.60% | 27.55% | CA -> C,CAA,CAAA AA,CAAAA,C AAA,CAAAAA AAAA | NA |
LOC_Os12g37680.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: CAAAAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os12g37680.1 Alt: CAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os12g37680.1 Alt: CAAA| frameshift_variant HIGH(snpEff) LOC_Os12g37690.1 Alt: CAAA| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37680.1 Alt: CAAAA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os12g37680.1 Alt: CAAAAAAAAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 87.011; most accessible tissue: Minghui63 flag leaf, score: 99.571 |
| vg1223130857 (J) | chr12 | 23130857 | A | T | 86.80% | 4.15% | A -> T | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 86.959; most accessible tissue: Minghui63 flag leaf, score: 99.554 |
| vg1223130858 (J) | chr12 | 23130858 | AC | A | 98.10% | 1.31% | AC -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 86.959; most accessible tissue: Minghui63 flag leaf, score: 99.554 |
| vg1223130859 (J) | chr12 | 23130859 | C | A | 84.80% | 13.56% | C -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 86.959; most accessible tissue: Minghui63 flag leaf, score: 99.554 |
| vg1223130860 (J) | chr12 | 23130860 | C | T | 99.50% | 0.51% | C -> T | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 86.949; most accessible tissue: Minghui63 flag leaf, score: 99.552 |
| vg1223130861 (J) | chr12 | 23130861 | T | A | 98.80% | 0.85% | T -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 86.945; most accessible tissue: Minghui63 flag leaf, score: 99.553 |
| vg1223130887 (J) | chr12 | 23130887 | G | T | 99.80% | 0.00% | G -> T,A | NA |
LOC_Os12g37680.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g37690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37680.1 Alt: T| synonymous_variant LOW(snpEff) LOC_Os12g37690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.170; most accessible tissue: Minghui63 flag leaf, score: 99.586 |
| vg1223130894 (J) | chr12 | 23130894 | G | A | 95.00% | 3.05% | G -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 87.215; most accessible tissue: Minghui63 flag leaf, score: 99.596 |
| vg1223130902 (J) | chr12 | 23130902 | G | A | 98.20% | 0.76% | G -> A | NA |
LOC_Os12g37680.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os12g37690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.082; most accessible tissue: Minghui63 flag leaf, score: 99.595 |
| vg1223130909 (J) | chr12 | 23130909 | G | A | 92.10% | 5.46% | G -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 87.560; most accessible tissue: Minghui63 flag leaf, score: 99.665 |
| vg1223130918 (J) | chr12 | 23130918 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g37690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 87.629; most accessible tissue: Minghui63 flag leaf, score: 99.682 |
| vg1223130943 (J) | chr12 | 23130943 | C | T | 53.00% | 34.91% | C -> T | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 89.373; most accessible tissue: Minghui63 flag leaf, score: 99.671 |
| vg1223130944 (J) | chr12 | 23130944 | C | T | 97.30% | 2.14% | C -> T | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 89.376; most accessible tissue: Minghui63 flag leaf, score: 99.672 |
| vg1223130989 (J) | chr12 | 23130989 | C | T | 52.60% | 36.31% | C -> T | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 89.690; most accessible tissue: Minghui63 flag leaf, score: 99.662 |
| vg1223130990 (J) | chr12 | 23130990 | G | A | 98.70% | 0.63% | G -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 89.691; most accessible tissue: Minghui63 flag leaf, score: 99.662 |
| vg1223131002 (J) | chr12 | 23131002 | C | T | 52.50% | 36.27% | C -> T | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 89.721; most accessible tissue: Minghui63 flag leaf, score: 99.660 |
| vg1223131010 (J) | chr12 | 23131010 | T | Unkown | 98.60% | 0.87% | T -> C | NA |
LOC_Os12g37680.1 Alt: C| synonymous_variant LOW(snpEff)
LOC_Os12g37690.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.834; most accessible tissue: Minghui63 flag leaf, score: 99.677 |
| vg1223131018 (J) | chr12 | 23131018 | C | T | 90.30% | 8.08% | C -> T | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 89.864; most accessible tissue: Minghui63 flag leaf, score: 99.673 |
| vg1223131024 (J) | chr12 | 23131024 | G | T | 98.90% | 0.25% | G -> T,A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff) LOC_Os12g37690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37680.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2) The average chromatin accessibility score: 89.878; most accessible tissue: Minghui63 flag leaf, score: 99.671 |
| vg1223131025 (J) | chr12 | 23131025 | C | T | 99.10% | 0.57% | C -> T | NA |
LOC_Os12g37680.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os12g37690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 89.834; most accessible tissue: Minghui63 flag leaf, score: 99.653 |
| vg1223131032 (J) | chr12 | 23131032 | C | Unkown | 99.30% | 0.59% | C -> T | NA |
LOC_Os12g37680.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os12g37690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.119; most accessible tissue: Minghui63 flag leaf, score: 99.687 |
| vg1223131044 (J) | chr12 | 23131044 | G | A | 70.50% | 19.19% | G -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 90.133; most accessible tissue: Minghui63 flag leaf, score: 99.685 |
| vg1223131047 (J) | chr12 | 23131047 | G | A | 98.60% | 0.61% | G -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 90.165; most accessible tissue: Minghui63 flag leaf, score: 99.687 |
| vg1223131059 (J) | chr12 | 23131059 | G | A | 71.10% | 18.58% | G -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 90.295; most accessible tissue: Minghui63 flag leaf, score: 99.711 |
| vg1223131066 (J) | chr12 | 23131066 | G | T | 99.80% | 0.00% | G -> A,T | NA |
LOC_Os12g37680.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os12g37690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os12g37680.1 Alt: T| missense_variant MODERATE(snpEff) LOC_Os12g37690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 90.350; most accessible tissue: Minghui63 flag leaf, score: 99.718 |
| vg1223131103 (J) | chr12 | 23131103 | G | A | 98.10% | 1.65% | G -> A | NA |
LOC_Os12g37680.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g37680.1 Alt: A| splice_region_variant&stop_retained_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 90.098; most accessible tissue: Minghui63 flag leaf, score: 99.720 |