20 variations found. LOC_Os05g18220 (retrotransposon protein; putative; unclassified), ranging from 10,478,232 bp to 10,478,916 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478333 (J) | chr05 | 10478333 | A | T | 91.30% | 0.11% | A -> T | NA |
LOC_Os05g18210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 20.555; most accessible tissue: Zhenshan97 flag leaf, score: 40.929 |
| vg0510478361 (J) | chr05 | 10478361 | C | T | 97.00% | 0.00% | C -> T | NA |
LOC_Os05g18210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 20.291; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 |
| vg0510478388 (J) | chr05 | 10478388 | G | A | 86.40% | 0.53% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g18210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18230.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 20.396; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 |
| vg0510478390 (J) | chr05 | 10478390 | T | A | 99.70% | 0.00% | T -> A | NA |
LOC_Os05g18210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g18230.1 Alt: A| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g18220.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 20.396; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 |
| vg0510478395 (J) | chr05 | 10478395 | A | T | 86.30% | 0.57% | A -> T | NA |
LOC_Os05g18210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 20.530; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 |
| vg0510478413 (J) | chr05 | 10478413 | A | G | 99.80% | 0.00% | A -> G | NA |
LOC_Os05g18210.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g18230.1 Alt: G| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g18220.1 Alt: G| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 19.475; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 |
| vg0510478441 (J) | chr05 | 10478441 | A | C | 99.50% | 0.00% | A -> C | NA |
LOC_Os05g18210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 18.928; most accessible tissue: Zhenshan97 flag leaf, score: 33.231 |
| vg0510478446 (J) | chr05 | 10478446 | G | A | 94.40% | 0.00% | G -> A | NA |
LOC_Os05g18210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 19.275; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 |
| vg0510478449 (J) | chr05 | 10478449 | T | C | 87.90% | 0.00% | T -> C | NA |
LOC_Os05g18210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 19.353; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 |
| vg0510478451 (J) | chr05 | 10478451 | T | C | 92.20% | 0.04% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g18210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18230.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 19.300; most accessible tissue: Zhenshan97 flag leaf, score: 35.167 |
| vg0510478458 (J) | chr05 | 10478458 | G | A | 91.00% | 0.04% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g18210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18230.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 19.712; most accessible tissue: Zhenshan97 flag leaf, score: 37.100 |
| vg0510478459 (J) | chr05 | 10478459 | T | C | 92.00% | 0.04% | T -> C | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g18210.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18230.1 Alt: C| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: C| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 19.712; most accessible tissue: Zhenshan97 flag leaf, score: 37.100 |
| vg0510478464 (J) | chr05 | 10478464 | T | A | 90.90% | 0.06% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g18210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18230.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 19.712; most accessible tissue: Zhenshan97 flag leaf, score: 37.100 |
| vg0510478732 (J) | chr05 | 10478732 | T | A | 97.10% | 0.00% | T -> A | NA |
LOC_Os05g18210.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 23.330; most accessible tissue: Zhenshan97 flag leaf, score: 45.537 |
| vg0510478743 (J) | chr05 | 10478743 | C | T | 90.30% | 0.00% | C -> T | NA |
LOC_Os05g18210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g18230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g18220.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 23.422; most accessible tissue: Zhenshan97 flag leaf, score: 46.427 |
| vg0510478778 (J) | chr05 | 10478778 | G | A | 91.10% | 0.00% | G -> A | NA |
LOC_Os05g18220.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 22.596; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 |
| vg0510478805 (J) | chr05 | 10478805 | T | C | 93.90% | 0.00% | T -> C | NA |
LOC_Os05g18220.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 22.481; most accessible tissue: Zhenshan97 flag leaf, score: 41.874 |
| vg0510478855 (J) | chr05 | 10478855 | C | T | 98.90% | 0.00% | C -> T | NA |
LOC_Os05g18220.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 22.198; most accessible tissue: Zhenshan97 flag leaf, score: 42.807 |
| vg0510478870 (J) | chr05 | 10478870 | C | T | 99.60% | 0.00% | C -> T | NA |
LOC_Os05g18220.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os05g18210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g18230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 23.125; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 |
| vg0510478875 (J) | chr05 | 10478875 | C | T | 99.80% | 0.00% | C -> T | NA |
LOC_Os05g18220.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os05g18210.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) LOC_Os05g18230.1 Alt: T| downstream_gene_variant MODIFIER(snpEff) The average chromatin accessibility score: 23.181; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 |