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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_Os02g05570 (transposon protein; putative; CACTA; En%2FSpm sub-class), ranging from 2,702,805 bp to 2,706,492 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
vg0202704838 (J) chr02 2704838 G A 27.70% 67.94% G -> A NA
LOC_Os02g05560.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05580.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os02g05570.1 Alt: A| intron_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 13.241; most accessible tissue: Minghui63 panicle, score: 29.741
vg0202706398 (J) chr02 2706398 G C 34.90% 63.56% G -> C NA
LOC_Os02g05570.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os02g05570.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 5.325; most accessible tissue: Minghui63 flag leaf, score: 10.316
vg0202706439 (J) chr02 2706439 G A 36.90% 59.69% G -> A NA
LOC_Os02g05570.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g05570.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.229; most accessible tissue: Minghui63 flower, score: 9.270