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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:

4 variations found. LOC_Os01g49500 (retrotransposon protein; putative; unclassified), ranging from 28,476,912 bp to 28,477,239 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
vg0128477000 (J) chr01 28477000 A G 31.60% 67.22% A -> G NA
LOC_Os01g49500.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g49500.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.966; most accessible tissue: Callus, score: 16.999
vg0128477180 (J) chr01 28477180 G A 29.10% 64.90% G -> A NA
LOC_Os01g49500.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os01g49500.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.814; most accessible tissue: Callus, score: 15.328
vg0128477193 (J) chr01 28477193 C T 30.30% 68.81% C -> T NA
LOC_Os01g49500.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os01g49500.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.814; most accessible tissue: Callus, score: 15.328
vg0128477203 (J) chr01 28477203 G A 30.50% 66.84% G -> A NA
LOC_Os01g49500.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os01g49500.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.724; most accessible tissue: Callus, score: 15.328