17 variations found. LOC_Os01g61090 (transposon protein; putative; unclassified; expressed), ranging from 35,352,790 bp to 35,360,344 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0135353033 (J) | chr01 | 35353033 | G | A | 23.80% | 72.98% | G -> A | NA |
LOC_Os01g61080.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g61090.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 17.275; most accessible tissue: Zhenshan97 root, score: 39.742 |
| vg0135353088 (J) | chr01 | 35353088 | A | G | 24.70% | 72.79% | A -> G | NA |
LOC_Os01g61080.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g61090.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 18.329; most accessible tissue: Zhenshan97 root, score: 41.416 |
| vg0135353524 (J) | chr01 | 35353524 | G | A | 24.10% | 63.46% | G -> A | NA |
LOC_Os01g61090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 18.798; most accessible tissue: Zhenshan97 flag leaf, score: 37.100 |
| vg0135356886 (J) | chr01 | 35356886 | G | A | 7.60% | 76.39% | G -> A | NA |
LOC_Os01g61090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 33.792; most accessible tissue: Zhenshan97 flag leaf, score: 75.143 |
| vg0135356924 (J) | chr01 | 35356924 | C | A | 12.30% | 75.12% | C -> A | NA |
LOC_Os01g61090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.934; most accessible tissue: Zhenshan97 flag leaf, score: 71.238 |
| vg0135356929 (J) | chr01 | 35356929 | G | A | 7.60% | 76.05% | G -> A | NA |
LOC_Os01g61090.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.931; most accessible tissue: Zhenshan97 flag leaf, score: 71.630 |
| vg0135356943 (J) | chr01 | 35356943 | A | G | 7.60% | 75.96% | A -> G | NA |
LOC_Os01g61090.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 32.766; most accessible tissue: Zhenshan97 flag leaf, score: 70.837 |
| vg0135357580 (J) | chr01 | 35357580 | C | G | 54.60% | 26.60% | C -> G | NA |
LOC_Os01g61100.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g61090.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.560; most accessible tissue: Zhenshan97 root, score: 32.766 |
| vg0135357594 (J) | chr01 | 35357594 | C | T | 47.40% | 26.64% | C -> T | NA |
LOC_Os01g61100.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os01g61090.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 10.560; most accessible tissue: Zhenshan97 root, score: 32.766 |
| vg0135357938 (J) | chr01 | 35357938 | TC | T | 24.70% | 73.13% | TC -> T | NA |
LOC_Os01g61090.1 Alt: T| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.480; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0135357941 (J) | chr01 | 35357941 | G | T | 24.70% | 73.13% | G -> T | NA |
LOC_Os01g61090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.003; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0135357942 (J) | chr01 | 35357942 | C | T | 24.80% | 72.96% | C -> T | NA |
LOC_Os01g61090.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.003; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0135357983 (J) | chr01 | 35357983 | C | T | 53.90% | 27.17% | C -> T | NA |
LOC_Os01g61090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 5.003; most accessible tissue: Zhenshan97 root, score: 10.511 |
| vg0135358024 (J) | chr01 | 35358024 | G | C | 55.00% | 27.04% | G -> C | NA |
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g61090.1 Alt: C| stop_gained HIGH(snpEff)/stop_gained(CooVar) The average chromatin accessibility score: 6.031; most accessible tissue: Zhenshan97 flower, score: 11.396 |
| vg0135358029 (J) | chr01 | 35358029 | G | A | 38.70% | 26.56% | G -> A | NA |
LOC_Os01g61090.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.214; most accessible tissue: Zhenshan97 flower, score: 11.396 |
| vg0135359483 (J) | chr01 | 35359483 | T | G | 24.60% | 71.22% | T -> G | NA |
LOC_Os01g61090.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 10.981; most accessible tissue: Zhenshan97 panicle, score: 32.308 |
| vg0135359915 (J) | chr01 | 35359915 | G | T | 36.30% | 60.52% | G -> T | NA |
LOC_Os01g61090.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g61090.1 Alt: DEL/frameshift_variant(CooVar) The average chromatin accessibility score: 6.643; most accessible tissue: Zhenshan97 panicle, score: 16.188 |