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Search Results:

2 variations found. LOC_Os02g49300 (transposon protein; putative; CACTA; En%2FSpm sub-class; expressed), ranging from 30,127,961 bp to 30,131,293 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
vg0230128709 (J) chr02 30128709 G A 37.90% 56.22% G -> A NA
LOC_Os02g49300.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os02g49300.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 13.318; most accessible tissue: Minghui63 root, score: 21.615
vg0230129626 (J) chr02 30129626 T Unkown 0.80% 95.77% C -> T NA
LOC_Os02g49300.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os02g49300.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.530; most accessible tissue: Minghui63 panicle, score: 7.125