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Search Results:

17 variations found. LOC_Os06g21050 (retrotransposon protein; putative; Ty3-gypsy subclass; expressed), ranging from 12,160,155 bp to 12,164,056 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
vg0612160189 (J) chr06 12160189 C T 83.30% 11.21% C -> T NA
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160192 (J) chr06 12160192 T C 83.40% 11.26% T -> C NA
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160194 (J) chr06 12160194 G A 83.20% 11.19% G -> A NA
LOC_Os06g21050.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160204 (J) chr06 12160204 C T 83.30% 11.51% C -> T NA
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160207 (J) chr06 12160207 A G 38.80% 1.27% A -> G NA
LOC_Os06g21050.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160212 (J) chr06 12160212 C T 82.40% 11.45% C -> T,A NA
LOC_Os06g21050.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g21050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160213 (J) chr06 12160213 C T 83.50% 11.24% C -> T NA
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160216 (J) chr06 12160216 A C 81.00% 11.45% A -> C NA
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160219 (J) chr06 12160219 T C 82.10% 11.11% T -> C NA
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160225 (J) chr06 12160225 C T 83.90% 10.81% C -> T NA
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160226 (J) chr06 12160226 G A 84.00% 10.58% G -> A NA
LOC_Os06g21050.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160228 (J) chr06 12160228 T C 84.20% 10.47% T -> C NA
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160237 (J) chr06 12160237 C T 80.40% 14.60% C -> T NA
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160243 (J) chr06 12160243 C A 45.80% 30.70% C -> T,A NA
LOC_Os06g21050.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160252 (J) chr06 12160252 G A 32.50% 46.11% G -> A NA
LOC_Os06g21050.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160258 (J) chr06 12160258 T C 38.00% 37.24% T -> C NA
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os06g21050.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991
vg0612160260 (J) chr06 12160260 G A 37.60% 38.68% G -> A NA
LOC_Os06g21050.1 Alt: A| stop_gained HIGH(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os06g21050.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.878; most accessible tissue: Callus, score: 8.991