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Search Results:

6 variations found. LOC_Os03g46424 (expressed protein), ranging from 26,251,598 bp to 26,251,847 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
vg0326251603 (J) chr03 26251603 C A 99.90% 0.00% C -> A NA
LOC_Os03g46424.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g46430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g46420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 87.103; most accessible tissue: Zhenshan97 flag leaf, score: 93.925
vg0326251743 (J) chr03 26251743 G Unkown 99.30% 0.66% G -> A NA
LOC_Os03g46424.1 Alt: A| missense_variant MODERATE(snpEff)
LOC_Os03g46430.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g46420.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 95.060; most accessible tissue: Zhenshan97 young leaf, score: 96.764
vg0326251773 (J) chr03 26251773 AG A 99.30% 0.66% AG -> A NA
LOC_Os03g46424.1 Alt: A| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g46424.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.679; most accessible tissue: Zhenshan97 young leaf, score: 97.142
vg0326251780 (J) chr03 26251780 CG C 99.30% 0.66% CG -> C NA
LOC_Os03g46424.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os03g46424.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.709; most accessible tissue: Zhenshan97 young leaf, score: 97.206
vg0326251790 (J) chr03 26251790 C T 99.30% 0.61% C -> T NA
LOC_Os03g46424.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os03g46424.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 95.973; most accessible tissue: Zhenshan97 young leaf, score: 97.435
vg0326251842 (J) chr03 26251842 A G 99.90% 0.00% A -> G NA
LOC_Os03g46424.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os03g46430.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)
LOC_Os03g46420.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 96.168; most accessible tissue: Minghui63 root, score: 97.651