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Search Results:

6 variations found. LOC_Os08g05150 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 2,666,437 bp to 2,670,679 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
vg0802667206 (J) chr08 2667206 T C 2.20% 69.85% C -> T NA
LOC_Os08g05150.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g05150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0802667623 (J) chr08 2667623 A Unkown 0.60% 74.65% G -> A NA
LOC_Os08g05150.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g05150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 15.079; most accessible tissue: Minghui63 young leaf, score: 22.423
vg0802668766 (J) chr08 2668766 C T 58.40% 25.39% C -> T NA
LOC_Os08g05150.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g05150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.896; most accessible tissue: Minghui63 flag leaf, score: 14.810
vg0802669982 (J) chr08 2669982 C T 71.30% 22.75% C -> T NA
LOC_Os08g05150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g05150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.210; most accessible tissue: Minghui63 panicle, score: 7.125
vg0802670291 (J) chr08 2670291 G T 74.90% 23.11% G -> T NA
LOC_Os08g05150.1 Alt: T/stop_gained(CooVar)
LOC_Os08g05150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.620; most accessible tissue: Minghui63 panicle, score: 20.733
vg0802670352 (J) chr08 2670352 C T 75.20% 20.97% C -> T NA
LOC_Os08g05150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g05150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 10.620; most accessible tissue: Minghui63 panicle, score: 20.733