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Search Results:

3 variations found. LOC_Os03g44636 (zinc finger; C3HC4 type domain containing protein; expressed), ranging from 25,135,529 bp to 25,136,081 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
vg0325135676 (J) chr03 25135676 A G 60.10% 0.00% G -> A
mr1107 (Ind_All); LR P-value: 6.17E-06;
mr1218 (All); LR P-value: 1.50E-14;
mr1336 (All); LR P-value: 5.48E-09;
mr1155_2 (All); LR P-value: 6.84E-39;
mr1336_2 (All); LR P-value: 5.86E-18;
mr1386_2 (All); LR P-value: 4.34E-25
LOC_Os03g44636.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 87.454; most accessible tissue: Zhenshan97 root, score: 94.212
vg0325135970 (J) chr03 25135970 CTGCCGC CGGCCAA C 59.50% 0.00% C -> CTGCCGCCGG CCAA,CTGCC GCCAGCCAA NA
LOC_Os03g44636.1 Alt: CTGCCGCCAGCCAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g44636.1 Alt: CTGCCGCCGGCCAA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 79.421; most accessible tissue: Minghui63 panicle, score: 90.408
vg0325135973 (J) chr03 25135973 C T 99.80% 0.00% C -> T NA
LOC_Os03g44636.1 Alt: T| synonymous_variant LOW(snpEff)
LOC_Os03g44630.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g44642.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g44620.2 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os03g44650.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 79.357; most accessible tissue: Minghui63 panicle, score: 90.408