19 variations found. LOC_Os11g39060 (expressed protein), ranging from 23,252,863 bp to 23,253,271 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1123252881 (J) | chr11 | 23252881 | C | T | 95.90% | 0.00% | C -> T | NA |
LOC_Os11g39060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.848; most accessible tissue: Minghui63 root, score: 81.505 |
| vg1123252909 (J) | chr11 | 23252909 | C | G | 91.70% | 0.00% | G -> C | NA |
LOC_Os11g39060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 65.748; most accessible tissue: Minghui63 root, score: 82.185 |
| vg1123252936 (J) | chr11 | 23252936 | ATCGGCG AGGTAGC TCTCGCC GACGACG TAGCAGC CGTTGTC CTCGACC TGGCGGC TGACC | GTCGGCG AGGTAGC TCTCGCC GACGACG TAGCAGC CGTTGTC CTCGACC TGGCGGC TGACC | 99.60% | 0.00% | ATCGGCGAGG TAGCTCTCGC CGACGACGTA GCAGCCGTTG TCCTCGACCT GGCGGCTGAC C -> GTCGGCGAGG TAGCTCTCGC CGACGACGTA GCAGCCGTTG TCCTCGACCT GGCGGCTGAC C,A | NA |
LOC_Os11g39060.1 Alt: GTCGGCGAGGTAGCTCTCGCCGACGACGTAGCAGCCGTTGTCCTCGACCTGGCGGCTGACC| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g39060.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 68.287; most accessible tissue: Callus, score: 83.174 |
| vg1123252949 (J) | chr11 | 23252949 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os11g39060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 68.777; most accessible tissue: Callus, score: 83.174 |
| vg1123252956 (J) | chr11 | 23252956 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os11g39060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 70.048; most accessible tissue: Callus, score: 83.174 |
| vg1123252981 (J) | chr11 | 23252981 | G | A | 99.70% | 0.00% | G -> A | NA |
LOC_Os11g39060.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os11g39040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39070.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.369; most accessible tissue: Callus, score: 83.174 |
| vg1123253110 (J) | chr11 | 23253110 | C | A | 99.90% | 0.00% | C -> A | NA |
LOC_Os11g39060.1 Alt: A| synonymous_variant LOW(snpEff)
LOC_Os11g39040.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39050.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39070.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.051; most accessible tissue: Minghui63 root, score: 83.538 |
| vg1123253132 (J) | chr11 | 23253132 | G | C | 97.70% | 0.00% | G -> C | NA |
LOC_Os11g39060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.246; most accessible tissue: Minghui63 root, score: 82.967 |
| vg1123253136 (J) | chr11 | 23253136 | G | C | 93.80% | 0.00% | G -> C | NA |
LOC_Os11g39060.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.076; most accessible tissue: Minghui63 root, score: 82.967 |
| vg1123253183 (J) | chr11 | 23253183 | G | C | 99.70% | 0.00% | G -> C | NA |
LOC_Os11g39060.1 Alt: C| missense_variant MODERATE(snpEff)
LOC_Os11g39040.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39050.1 Alt: C| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39070.1 Alt: C| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 70.061; most accessible tissue: Minghui63 root, score: 82.818 |
| vg1123253199 (J) | chr11 | 23253199 | C | T | 99.00% | 0.00% | C -> T | NA |
LOC_Os11g39060.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 69.645; most accessible tissue: Callus, score: 82.581 |
| vg1123253205 (J) | chr11 | 23253205 | C | G | 97.30% | 0.00% | C -> G | NA |
LOC_Os11g39060.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 69.249; most accessible tissue: Callus, score: 82.581 |
| vg1123253212 (J) | chr11 | 23253212 | G | A | 95.30% | 0.19% | G -> A,C | NA |
LOC_Os11g39060.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g39060.1 Alt: DEL/frameshift_variant(CooVar) LOC_Os11g39060.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar) The average chromatin accessibility score: 69.470; most accessible tissue: Callus, score: 82.581 |
| vg1123253223 (J) | chr11 | 23253223 | C | CCGT | 97.70% | 0.00% | C -> CCGT,T | NA |
LOC_Os11g39060.1 Alt: CCGT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os11g39060.1 Alt: T| missense_variant MODERATE(snpEff) LOC_Os11g39040.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39050.1 Alt: T| upstream_gene_variant MODIFIER(snpEff) LOC_Os11g39070.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 69.352; most accessible tissue: Callus, score: 82.581 |
| vg1123253227 (J) | chr11 | 23253227 | C | T | 97.90% | 0.00% | C -> T | NA |
LOC_Os11g39060.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.551; most accessible tissue: Callus, score: 82.581 |
| vg1123253254 (J) | chr11 | 23253254 | C | CTCGTCG GCTGATG CCAAGTG AAT | 97.10% | 0.00% | C -> CTCGTCGGCT GATGCCAAGT GAAT,CTCGT CGGCTG,CAA GTGAAT | NA |
LOC_Os11g39060.1 Alt: CTCGTCGGCTGATGCCAAGTGAAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g39060.1 Alt: CAAGTGAAT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) LOC_Os11g39060.1 Alt: CTCGTCGGCTG| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar) The average chromatin accessibility score: 68.695; most accessible tissue: Callus, score: 82.581 |
| vg1123253256 (J) | chr11 | 23253256 | C | CTGATCC ATCATCC ATGGA | 97.10% | 0.00% | C -> CTGATCCATC ATCCATGGA, CTGATCCATC ATCCATGGAC GCCTCGT | NA |
LOC_Os11g39060.1 Alt: CTGATCCATCATCCATGGACGCCTCGT| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os11g39060.1 Alt: CTGATCCATCATCCATGGA| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar) The average chromatin accessibility score: 68.634; most accessible tissue: Callus, score: 82.581 |
| vg1123253259 (J) | chr11 | 23253259 | C | CCTCGTC GTCTTCT TTGCCTC GTCGGCG | 97.10% | 0.00% | C -> CCTCGTCGTC TTCTTTGCCT CGTCGGCG | NA |
LOC_Os11g39060.1 Alt: CCTCGTCGTCTTCTTTGCCTCGTCGGCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 69.310; most accessible tissue: Callus, score: 82.581 |
| STR1123253213 (J) | chr11 | 23253213 | GCCGCCG CCGCCG | GCCGCCG CCGCCGC CG | 93.80% | 0.00% | GCCGCCGCCG CCG -> GCCGCCGCCG CCGCCG | NA |
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