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Search Results:

5 variations found. LOC_Os04g24640 (retrotransposon protein; putative; unclassified), ranging from 14,145,582 bp to 14,147,103 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
vg0414145678 (J) chr04 14145678 C T 24.80% 64.18% C -> T NA
LOC_Os04g24640.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g24640.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 24.211; most accessible tissue: Zhenshan97 flag leaf, score: 68.250
vg0414145792 (J) chr04 14145792 G A 37.30% 57.43% G -> A NA
LOC_Os04g24640.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g24640.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 16.389; most accessible tissue: Zhenshan97 flag leaf, score: 41.874
vg0414145962 (J) chr04 14145962 T G 22.60% 67.14% T -> G NA
LOC_Os04g24640.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g24640.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 10.323; most accessible tissue: Zhenshan97 root, score: 25.639
vg0414146540 (J) chr04 14146540 A C 6.40% 75.45% A -> C NA
LOC_Os04g24640.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os04g24640.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.793; most accessible tissue: Zhenshan97 flag leaf, score: 7.948
vg0414146616 (J) chr04 14146616 T C 0.30% 85.21% C -> T NA
LOC_Os04g24640.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os04g24640.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 4.779; most accessible tissue: Zhenshan97 flag leaf, score: 7.948