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Search Results:

37 variations found. LOC_Os08g27910 (retrotransposon protein; putative; unclassified; expressed), ranging from 17,014,592 bp to 17,016,026 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
vg0817014728 (J) chr08 17014728 G A 54.90% 42.55% G -> A NA
LOC_Os08g27910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.547; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0817014758 (J) chr08 17014758 T C 21.90% 43.65% T -> C NA
LOC_Os08g27910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.547; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0817014770 (J) chr08 17014770 C A 56.40% 41.90% C -> A NA
LOC_Os08g27910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.547; most accessible tissue: Zhenshan97 flower, score: 9.663
vg0817014780 (J) chr08 17014780 C T 56.10% 42.09% C -> T NA
LOC_Os08g27910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.677; most accessible tissue: Minghui63 panicle, score: 7.125
vg0817014784 (J) chr08 17014784 A G 18.00% 45.18% A -> G NA
LOC_Os08g27910.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.677; most accessible tissue: Minghui63 panicle, score: 7.125
vg0817014785 (J) chr08 17014785 G A 56.10% 42.11% G -> A NA
LOC_Os08g27910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.677; most accessible tissue: Minghui63 panicle, score: 7.125
vg0817014807 (J) chr08 17014807 C T 19.20% 49.83% C -> T NA
LOC_Os08g27910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.677; most accessible tissue: Minghui63 panicle, score: 7.125
vg0817015064 (J) chr08 17015064 C T 22.70% 49.89% C -> T NA
LOC_Os08g27910.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.717; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015133 (J) chr08 17015133 T C 44.90% 46.78% T -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.832; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015139 (J) chr08 17015139 G A 43.20% 46.87% G -> A NA
LOC_Os08g27910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.832; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015182 (J) chr08 17015182 A G 17.90% 67.67% A -> G NA
LOC_Os08g27910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.995; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015495 (J) chr08 17015495 A G 46.30% 46.30% A -> T,G NA
LOC_Os08g27910.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.760; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015519 (J) chr08 17015519 C T 43.60% 46.87% C -> T NA
LOC_Os08g27910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.760; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015555 (J) chr08 17015555 C T 23.70% 52.75% C -> T NA
LOC_Os08g27910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.760; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015584 (J) chr08 17015584 C T 23.00% 50.78% C -> T NA
LOC_Os08g27910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.759; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015603 (J) chr08 17015603 C T 23.70% 48.60% C -> T NA
LOC_Os08g27910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.759; most accessible tissue: Minghui63 panicle, score: 16.270
vg0817015679 (J) chr08 17015679 G A 23.50% 51.42% G -> A NA
LOC_Os08g27910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.770; most accessible tissue: Callus, score: 12.960
vg0817015804 (J) chr08 17015804 G C 24.60% 50.08% G -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.770; most accessible tissue: Callus, score: 12.960
vg0817015809 (J) chr08 17015809 T C 17.40% 69.04% T -> C,G NA
LOC_Os08g27910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.770; most accessible tissue: Callus, score: 12.960
vg0817015824 (J) chr08 17015824 A C 17.80% 69.13% A -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.953; most accessible tissue: Callus, score: 12.960
vg0817015825 (J) chr08 17015825 A C 18.00% 66.76% A -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.953; most accessible tissue: Callus, score: 12.960
vg0817015837 (J) chr08 17015837 C T 20.90% 69.02% C -> T NA
LOC_Os08g27910.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015840 (J) chr08 17015840 G T 19.00% 65.00% G -> T NA
LOC_Os08g27910.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015841 (J) chr08 17015841 T C 20.90% 67.56% T -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015851 (J) chr08 17015851 T C 21.60% 61.64% T -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015853 (J) chr08 17015853 A G 32.40% 48.71% A -> G NA
LOC_Os08g27910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015857 (J) chr08 17015857 T C 32.20% 48.71% T -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015858 (J) chr08 17015858 T C 32.10% 48.77% T -> C NA
LOC_Os08g27910.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015873 (J) chr08 17015873 T A 31.00% 50.04% T -> A NA
LOC_Os08g27910.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015877 (J) chr08 17015877 G T 30.70% 50.28% G -> T NA
LOC_Os08g27910.1 Alt: T| stop_gained HIGH(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015878 (J) chr08 17015878 A C 30.50% 50.40% A -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015894 (J) chr08 17015894 A G 30.60% 50.55% A -> G NA
LOC_Os08g27910.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015895 (J) chr08 17015895 A G 30.20% 50.53% A -> G NA
LOC_Os08g27910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015904 (J) chr08 17015904 C G 30.30% 50.78% C -> G NA
LOC_Os08g27910.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015909 (J) chr08 17015909 A C 20.10% 67.56% A -> C NA
LOC_Os08g27910.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.698; most accessible tissue: Callus, score: 10.152
vg0817015931 (J) chr08 17015931 T C 16.80% 68.92% T -> C NA
LOC_Os08g27910.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.214; most accessible tissue: Callus, score: 15.831
vg0817016017 (J) chr08 17016017 G A 34.10% 49.11% G -> A NA
LOC_Os08g27910.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os08g27910.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.824; most accessible tissue: Callus, score: 15.831