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Search Results:

4 variations found. LOC_Os12g11610 (expressed protein), ranging from 6,299,655 bp to 6,299,862 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
vg1206299767 (J) chr12 6299767 T C 21.50% 65.49% C -> T NA
LOC_Os12g11610.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11610.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.886; most accessible tissue: Zhenshan97 panicle, score: 79.799
vg1206299802 (J) chr12 6299802 G T 21.60% 65.30% T -> G NA
LOC_Os12g11610.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11610.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 67.801; most accessible tissue: Zhenshan97 panicle, score: 81.752
vg1206299819 (J) chr12 6299819 G T 21.50% 65.68% T -> G NA
LOC_Os12g11610.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11610.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 68.606; most accessible tissue: Zhenshan97 panicle, score: 82.888
vg1206299825 (J) chr12 6299825 A G 35.00% 61.55% A -> G NA
LOC_Os12g11610.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11610.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 68.350; most accessible tissue: Zhenshan97 panicle, score: 82.336