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Search Results:

6 variations found. LOC_Os09g25110 (transposon protein; putative; unclassified), ranging from 15,031,072 bp to 15,034,300 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
vg0915031255 (J) chr09 15031255 C T 13.00% 85.95% C -> T NA
LOC_Os09g25110.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g25110.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 10.189; most accessible tissue: Minghui63 panicle, score: 20.733
vg0915031657 (J) chr09 15031657 G T 13.10% 85.27% G -> T NA
LOC_Os09g25110.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g25110.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 7.723; most accessible tissue: Minghui63 root, score: 17.665
vg0915032738 (J) chr09 15032738 G A 10.70% 85.19% G -> A NA
LOC_Os09g25110.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g25110.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 4.785; most accessible tissue: Zhenshan97 flag leaf, score: 7.948
vg0915034003 (J) chr09 15034003 T C 11.70% 83.24% T -> C NA
LOC_Os09g25110.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g25110.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 4.470; most accessible tissue: Minghui63 panicle, score: 7.125
vg0915034277 (J) chr09 15034277 G A 17.80% 73.78% G -> A NA
LOC_Os09g25110.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g25110.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0915034284 (J) chr09 15034284 T C 18.20% 69.78% T -> C NA
LOC_Os09g25110.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g25110.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125