7 variations found. LOC_Os05g16340 (transposon protein; putative; CACTA; En%2FSpm sub-class), ranging from 9,253,172 bp to 9,254,600 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0509254050 (J) | chr05 | 9254050 | A | G | 0.40% | 64.85% | G -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g16330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g16340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 13.768; most accessible tissue: Zhenshan97 panicle, score: 20.424 |
| vg0509254201 (J) | chr05 | 9254201 | T | A | 94.30% | 1.76% | T -> A | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g16330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g16340.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 14.122; most accessible tissue: Zhenshan97 flag leaf, score: 21.748 |
| vg0509254204 (J) | chr05 | 9254204 | T | G | 94.30% | 1.61% | T -> G | NA |
N Alt: DEL/silent_mutation(CooVar)
LOC_Os05g16330.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar) LOC_Os05g16340.1 Alt: G| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) The average chromatin accessibility score: 14.694; most accessible tissue: Zhenshan97 panicle, score: 24.575 |
| vg0509254267 (J) | chr05 | 9254267 | C | Unkown | 91.00% | 5.71% | C -> A | NA |
LOC_Os05g16330.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os05g16340.1 Alt: A| intron_variant MODIFIER(snpEff) The average chromatin accessibility score: 16.798; most accessible tissue: Zhenshan97 flag leaf, score: 28.494 |
| vg0509254308 (J) | chr05 | 9254308 | C | T | 92.50% | 5.29% | C -> T | NA |
LOC_Os05g16330.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os05g16340.1 Alt: T| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar) N Alt: DEL/silent_mutation(CooVar) The average chromatin accessibility score: 19.293; most accessible tissue: Zhenshan97 panicle, score: 36.038 |
| vg0509254430 (J) | chr05 | 9254430 | G | A | 90.00% | 6.67% | G -> A | NA |
LOC_Os05g16340.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g16340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2) The average chromatin accessibility score: 28.285; most accessible tissue: Zhenshan97 panicle, score: 49.416 |
| vg0509254556 (J) | chr05 | 9254556 | G | A | 90.50% | 6.24% | G -> A | NA |
LOC_Os05g16340.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g16340.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar) The average chromatin accessibility score: 28.529; most accessible tissue: Zhenshan97 panicle, score: 52.263 |