26 variations found. LOC_Os11g09710 (expressed protein), ranging from 5,182,411 bp to 5,184,048 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105182696 (J) | chr11 | 5182696 | G | A | 64.60% | 31.00% | G -> A | NA |
LOC_Os11g09710.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 14.345; most accessible tissue: Callus, score: 85.245 |
| vg1105182729 (J) | chr11 | 5182729 | TGAGCTA | T | 64.40% | 30.79% | TGAGCTA -> T | NA |
LOC_Os11g09710.1 Alt: T| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.899; most accessible tissue: Callus, score: 85.245 |
| vg1105182879 (J) | chr11 | 5182879 | CTG | C | 68.40% | 29.94% | CTG -> C | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 10.920; most accessible tissue: Callus, score: 56.210 |
| vg1105183067 (J) | chr11 | 5183067 | A | C | 62.80% | 31.15% | A -> C |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: C| missense_variant&splice_region_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 11.644; most accessible tissue: Callus, score: 71.063 |
|
| vg1105183188 (J) | chr11 | 5183188 | C | CTTTT | 64.10% | 31.08% | C -> CTTTT,CTTT ,CTT | NA |
LOC_Os11g09720.1 Alt: CTTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09700.1 Alt: CTTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09710.1 Alt: CTTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09720.1 Alt: CTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09700.1 Alt: CTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09710.1 Alt: CTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09720.1 Alt: CTTT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09700.1 Alt: CTTT| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09710.1 Alt: CTTT| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 16.356; most accessible tissue: Callus, score: 81.049 |
| vg1105183232 (J) | chr11 | 5183232 | C | A | 66.80% | 30.64% | C -> A | NA |
LOC_Os11g09720.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09700.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os11g09710.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 16.484; most accessible tissue: Callus, score: 81.049 |
| vg1105183275 (J) | chr11 | 5183275 | A | G | 68.70% | 30.24% | A -> G | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 16.421; most accessible tissue: Callus, score: 81.049 |
| vg1105183353 (J) | chr11 | 5183353 | A | G | 62.70% | 31.06% | A -> G |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 15.540; most accessible tissue: Callus, score: 72.073 |
|
| vg1105183356 (J) | chr11 | 5183356 | A | C | 48.80% | 31.04% | A -> C | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 15.540; most accessible tissue: Callus, score: 72.073 |
| vg1105183431 (J) | chr11 | 5183431 | C | T | 57.70% | 32.23% | T -> C | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2) The average chromatin accessibility score: 17.689; most accessible tissue: Callus, score: 92.298 |
| vg1105183588 (J) | chr11 | 5183588 | C | T | 64.10% | 31.08% | C -> T | NA |
LOC_Os11g09710.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 13.132; most accessible tissue: Callus, score: 83.164 |
| vg1105183667 (J) | chr11 | 5183667 | A | G | 64.20% | 30.87% | A -> G | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 13.071; most accessible tissue: Callus, score: 83.164 |
| vg1105183725 (J) | chr11 | 5183725 | G | C | 66.80% | 30.81% | G -> C | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 17.630; most accessible tissue: Callus, score: 89.679 |
| vg1105183811 (J) | chr11 | 5183811 | T | TGG | 66.60% | 30.19% | T -> TGGGAG,TGG GAGAATTTAC TCTATGCCAC TCTACCAAAA TGGCAGTTCC C,TGG,TGGG AGAATTTACT CTATGCCACT CTACC,TGGG AGAATTTACT CTATGCCACT CTACCAAAAT GGC,TGGGAG AATTTACTCT ATGCCACTCT ACCAAAATGG CAGTTCCCAA ATGCC | NA |
LOC_Os11g09710.1 Alt: TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: TGG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os11g09710.1 Alt: TGGGAG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: TGGGAGAATTTACTCTATGCCACTCTACC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: TGGGAGAATTTACTCTATGCCACTCTACCAAAATGGCAGTTCCCAAATGCC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 18.184; most accessible tissue: Callus, score: 89.679 |
| vg1105183812 (J) | chr11 | 5183812 | A | G | 67.80% | 30.32% | A -> G | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 18.184; most accessible tissue: Callus, score: 89.679 |
| vg1105183831 (J) | chr11 | 5183831 | C | CAG | 48.70% | 30.81% | C -> CAG | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: CAG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 15.265; most accessible tissue: Callus, score: 53.099 |
| vg1105183835 (J) | chr11 | 5183835 | CTT | C | 67.50% | 30.41% | CTT -> C,TTT | NA |
LOC_Os11g09710.1 Alt: TTT| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 15.412; most accessible tissue: Callus, score: 53.099 |
| vg1105183878 (J) | chr11 | 5183878 | AGGGG | ACTCTGG GG | 9.90% | 44.60% | AGGGG -> ACTCTGGCAT GGGG,ACTCT GGGG,ACTCT GGCATGAGTA GCTTAAGCTT TGGGG,ACTC TGGCATGAGT AGCTTAAGCT TTGGTGGGG, A | NA |
LOC_Os11g09710.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: ACTCTGGCATGAGTAGCTTAAGCTTTGGGG| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: ACTCTGGCATGGGG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) LOC_Os11g09710.1 Alt: ACTCTGGCATGAGTAGCTTAAGCTTTGGTGGGG| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: ACTCTGGGG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 18.986; most accessible tissue: Callus, score: 53.099 |
| vg1105183880 (J) | chr11 | 5183880 | G | GCATGAG TAGCTTA AGCTTT | 9.90% | 71.60% | G -> GCAT,GCATG AGTAGCTTAA GCTTT | NA |
LOC_Os11g09710.1 Alt: GCAT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g09710.1 Alt: GCATGAGTAGCTTAAGCTTT| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.337; most accessible tissue: Callus, score: 53.099 |
| vg1105183881 (J) | chr11 | 5183881 | G | GAGTA | 10.30% | 68.13% | G -> GAGTA,T,A | NA |
LOC_Os11g09710.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os11g09710.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) LOC_Os11g09710.1 Alt: GAGTA| frameshift_variant&stop_gained HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.337; most accessible tissue: Callus, score: 53.099 |
| vg1105183882 (J) | chr11 | 5183882 | G | GTGGAGA | 10.30% | 74.38% | G -> GTGGAGA,C | NA |
LOC_Os11g09710.1 Alt: GTGGAGA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 19.337; most accessible tissue: Callus, score: 53.099 |
| vg1105183884 (J) | chr11 | 5183884 | T | TTAA | 9.90% | 86.46% | T -> TTAA | NA |
LOC_Os11g09710.1 Alt: TTAA| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.337; most accessible tissue: Callus, score: 53.099 |
| vg1105183885 (J) | chr11 | 5183885 | G | C | 9.90% | 81.85% | G -> GC,C | NA |
LOC_Os11g09710.1 Alt: GC| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g09710.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 19.337; most accessible tissue: Callus, score: 53.099 |
| vg1105183890 (J) | chr11 | 5183890 | G | GTGGAGA CTTA | 10.00% | 85.87% | G -> GTGGAGACTT A | NA |
LOC_Os11g09710.1 Alt: GTGGAGACTTA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.337; most accessible tissue: Callus, score: 53.099 |
| vg1105183894 (J) | chr11 | 5183894 | C | CTGG | 10.10% | 85.63% | C -> CTGG | NA |
LOC_Os11g09710.1 Alt: CTGG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 19.676; most accessible tissue: Callus, score: 53.099 |
| vg1105183896 (J) | chr11 | 5183896 | A | ATGAGTA GCTTAGT CTTTGGT G | 10.00% | 85.93% | A -> ATGAGTAGCT TAGTCTTTGG TG | NA |
LOC_Os11g09710.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09710.1 Alt: ATGAGTAGCTTAGTCTTTGGTG| disruptive_inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 19.676; most accessible tissue: Callus, score: 53.099 |