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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:

4 variations found. LOC_Os06g05030 (retrotransposon protein; putative; unclassified; expressed), ranging from 2,218,372 bp to 2,221,632 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
vg0602220450 (J) chr06 2220450 TAAG T 42.80% 52.69% TAAG -> T NA
LOC_Os06g05030.1 Alt: T| inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os06g05030.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 15.819; most accessible tissue: Minghui63 root, score: 45.031
vg0602220614 (J) chr06 2220614 A T 0.90% 86.39% A -> T NA
LOC_Os06g05030.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g05030.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 18.749; most accessible tissue: Minghui63 root, score: 50.524
vg0602220620 (J) chr06 2220620 C T 0.60% 92.74% C -> T NA
LOC_Os06g05030.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g05030.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 18.749; most accessible tissue: Minghui63 root, score: 50.524
vg0602220624 (J) chr06 2220624 T A 0.40% 93.10% T -> A NA
LOC_Os06g05030.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g05030.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 19.045; most accessible tissue: Minghui63 root, score: 50.524