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Search Results:

12 variations found. LOC_Os12g11620 (expressed protein), ranging from 6,301,851 bp to 6,302,061 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
vg1206301873 (J) chr12 6301873 T A 71.90% 20.36% T -> A NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 69.842; most accessible tissue: Zhenshan97 flag leaf, score: 83.366
vg1206301881 (J) chr12 6301881 A T 72.00% 20.36% A -> T NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 70.056; most accessible tissue: Zhenshan97 flag leaf, score: 83.526
vg1206301890 (J) chr12 6301890 C CTGAAAT 72.10% 22.85% C -> CTGAAAT NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: CTGAAAT| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 69.439; most accessible tissue: Zhenshan97 flag leaf, score: 83.205
vg1206301893 (J) chr12 6301893 G GA 73.20% 20.42% G -> GA NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: GA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 69.335; most accessible tissue: Zhenshan97 flag leaf, score: 82.703
vg1206301896 (J) chr12 6301896 T TGGATA 71.90% 20.42% T -> A,TGGATA NA
LOC_Os12g11620.1 Alt: TGGATA| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 69.517; most accessible tissue: Zhenshan97 flag leaf, score: 82.874
vg1206301922 (J) chr12 6301922 A T 71.80% 20.74% A -> T,G NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os12g11620.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 70.093; most accessible tissue: Zhenshan97 flag leaf, score: 82.874
vg1206301923 (J) chr12 6301923 G GATC 77.90% 20.84% G -> GATC NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: GATC| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 70.164; most accessible tissue: Zhenshan97 flag leaf, score: 82.874
vg1206301963 (J) chr12 6301963 C A 43.20% 38.70% C -> A NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 75.764; most accessible tissue: Zhenshan97 flag leaf, score: 84.864
vg1206301973 (J) chr12 6301973 A T 29.10% 54.57% T -> A NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 76.145; most accessible tissue: Zhenshan97 flag leaf, score: 85.259
vg1206301989 (J) chr12 6301989 T A 40.20% 56.07% T -> A NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 77.574; most accessible tissue: Zhenshan97 flag leaf, score: 86.230
vg1206302047 (J) chr12 6302047 G A 62.90% 26.96% G -> A NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 79.691; most accessible tissue: Zhenshan97 flag leaf, score: 87.661
vg1206302051 (J) chr12 6302051 G A 39.90% 44.35% G -> A NA
LOC_Os12g11620.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os12g11620.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 79.298; most accessible tissue: Zhenshan97 flag leaf, score: 87.567