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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

3 variations found. LOC_Os06g24360 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 14,256,161 bp to 14,260,384 bp (including 0 kb upstream and 0 kb downstream of the gene).

Variation Map (with Chromatin Accessibility Map/ Non-coding Varation Scores Map) in Searched Region:

The 'big effect' variations are marked out:

ColorExplainDetails
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.

Detailed Variation Information:

Var ID Chrom Position Primary Allele Secondary Allele Primary Allele Frequency DEL Frequency Var GWAS Results Effect
vg0614257025 (J) chr06 14257025 C T 31.70% 65.30% C -> T NA
LOC_Os06g24360.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g24360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.246; most accessible tissue: Callus, score: 13.035
vg0614257695 (J) chr06 14257695 A G 19.70% 62.10% A -> G NA
LOC_Os06g24360.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g24360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.741; most accessible tissue: Zhenshan97 flag leaf, score: 9.474
vg0614258037 (J) chr06 14258037 G A 32.10% 64.73% G -> A NA
LOC_Os06g24360.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g24360.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.366; most accessible tissue: Minghui63 panicle, score: 7.125