13 variations found. LOC_Os01g09220 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 4,646,426 bp to 4,648,260 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0104646629 (J) | chr01 | 4646629 | C | CGGCGGC GGT | 72.40% | 0.00% | C -> CGGCGGCGGT | NA |
LOC_Os01g09220.1 Alt: CGGCGGCGGT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 98.254; most accessible tissue: Zhenshan97 flag leaf, score: 99.949 |
| vg0104646744 (J) | chr01 | 4646744 | G | T | 97.00% | 0.00% | G -> T | NA |
LOC_Os01g09220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 98.580; most accessible tissue: Zhenshan97 flag leaf, score: 99.942 |
| vg0104646923 (J) | chr01 | 4646923 | C | T | 79.30% | 0.00% | C -> T | NA |
LOC_Os01g09220.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 96.387; most accessible tissue: Zhenshan97 flag leaf, score: 99.943 |
| vg0104647140 (J) | chr01 | 4647140 | T | C | 63.80% | 0.00% | C -> T |
LOC_Os01g09220.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 95.560; most accessible tissue: Minghui63 flag leaf, score: 99.926 |
|
| vg0104647200 (J) | chr01 | 4647200 | G | A | 71.10% | 0.23% | G -> A |
LOC_Os01g09220.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g09220.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 97.317; most accessible tissue: Minghui63 flag leaf, score: 99.922 |
|
| vg0104647221 (J) | chr01 | 4647221 | G | A | 71.10% | 0.13% | G -> A |
LOC_Os01g09220.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g09220.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 97.326; most accessible tissue: Minghui63 flag leaf, score: 99.928 |
|
| vg0104647379 (J) | chr01 | 4647379 | C | A | 85.40% | 0.00% | C -> A | NA |
LOC_Os01g09220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 94.910; most accessible tissue: Minghui63 flag leaf, score: 99.925 |
| vg0104647545 (J) | chr01 | 4647545 | G | A | 97.60% | 0.00% | G -> A | NA |
LOC_Os01g09220.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 97.471; most accessible tissue: Zhenshan97 young leaf, score: 99.937 |
| vg0104647828 (J) | chr01 | 4647828 | A | T | 95.90% | 0.00% | T -> A | NA |
LOC_Os01g09220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 95.410; most accessible tissue: Zhenshan97 young leaf, score: 99.898 |
| vg0104647843 (J) | chr01 | 4647843 | G | A | 99.80% | 0.00% | G -> A | NA |
LOC_Os01g09220.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os01g09206.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g09212.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) LOC_Os01g09230.1 Alt: A| upstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 95.338; most accessible tissue: Minghui63 flag leaf, score: 99.895 |
| vg0104648013 (J) | chr01 | 4648013 | A | AT | 87.90% | 0.00% | A -> AT | NA |
LOC_Os01g09220.1 Alt: AT| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g09206.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g09212.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g09230.1 Alt: AT| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 95.880; most accessible tissue: Minghui63 flag leaf, score: 99.845 |
| vg0104648042 (J) | chr01 | 4648042 | GT | G | 50.70% | 0.02% | GT -> G | NA |
LOC_Os01g09220.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g09206.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g09212.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g09230.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 95.345; most accessible tissue: Minghui63 flag leaf, score: 99.809 |
| vg0104648100 (J) | chr01 | 4648100 | T | C | 71.00% | 0.06% | T -> C |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os01g09220.1 Alt: C| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g09206.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g09212.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os01g09230.1 Alt: C| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 93.379; most accessible tissue: Minghui63 flag leaf, score: 99.763 |