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Search Results:

4 variations found. LOC_Os02g17110 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 9,796,797 bp to 9,800,498 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
vg0209796835 (J) chr02 9796835 C T 16.20% 66.80% C -> T NA
LOC_Os02g17110.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g17110.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.777; most accessible tissue: Zhenshan97 flag leaf, score: 13.342
vg0209796881 (J) chr02 9796881 C T 66.60% 31.40% C -> T NA
LOC_Os02g17110.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g17110.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.973; most accessible tissue: Zhenshan97 flower, score: 12.818
vg0209796925 (J) chr02 9796925 G A 66.80% 31.15% G -> A NA
LOC_Os02g17110.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os02g17110.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.689; most accessible tissue: Zhenshan97 flower, score: 12.818
vg0209797014 (J) chr02 9797014 G T 0.80% 70.63% G -> T NA
LOC_Os02g17110.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os02g17110.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.689; most accessible tissue: Zhenshan97 flower, score: 12.818