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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_Os06g04770 (transposon protein; putative; unclassified; expressed), ranging from 2,077,563 bp to 2,083,611 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
vg0602082808 (J) chr06 2082808 G A 0.50% 98.05% G -> A NA
LOC_Os06g04770.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g04770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 24.467; most accessible tissue: Minghui63 young leaf, score: 49.581
vg0602082830 (J) chr06 2082830 T C 0.50% 98.18% T -> C NA
LOC_Os06g04770.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g04770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 24.353; most accessible tissue: Minghui63 young leaf, score: 49.581
vg0602082832 (J) chr06 2082832 C T 0.50% 98.20% C -> T NA
LOC_Os06g04770.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g04770.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 24.353; most accessible tissue: Minghui63 young leaf, score: 49.581