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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_Os05g14460 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 8,166,932 bp to 8,170,633 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
vg0508168782 (J) chr05 8168782 G A 26.60% 47.00% G -> A NA
LOC_Os05g14460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g14460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 9.572; most accessible tissue: Zhenshan97 root, score: 15.132
vg0508168878 (J) chr05 8168878 A G 51.80% 30.34% A -> G NA
LOC_Os05g14460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g14460.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 10.758; most accessible tissue: Zhenshan97 flag leaf, score: 18.298
vg0508169154 (J) chr05 8169154 G A 49.10% 36.99% G -> A NA
LOC_Os05g14460.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os05g14460.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 8.563; most accessible tissue: Zhenshan97 flag leaf, score: 13.342