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Search Results:

19 variations found. LOC_Os11g17200 (retrotransposon protein; putative; Ty1-copia subclass; expressed), ranging from 9,581,775 bp to 9,585,684 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
vg1109582086 (J) chr11 9582086 G A 32.80% 24.84% G -> A NA
LOC_Os11g17200.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976
vg1109582115 (J) chr11 9582115 C T 33.80% 25.07% C -> T NA
LOC_Os11g17200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.769; most accessible tissue: Minghui63 young leaf, score: 9.976
vg1109582515 (J) chr11 9582515 G A 34.00% 24.14% G -> A NA
LOC_Os11g17200.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.359; most accessible tissue: Minghui63 panicle, score: 7.125
vg1109583675 (J) chr11 9583675 C T 33.30% 25.31% C -> T NA
LOC_Os11g17200.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.368; most accessible tissue: Callus, score: 14.376
vg1109584686 (J) chr11 9584686 C T 14.80% 43.25% C -> T NA
LOC_Os11g17200.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.595; most accessible tissue: Minghui63 panicle, score: 7.125
vg1109584715 (J) chr11 9584715 G A 58.60% 11.87% G -> A NA
LOC_Os11g17200.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.595; most accessible tissue: Minghui63 panicle, score: 7.125
vg1109584718 (J) chr11 9584718 C T 51.90% 29.96% C -> T NA
LOC_Os11g17200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.595; most accessible tissue: Minghui63 panicle, score: 7.125
vg1109584726 (J) chr11 9584726 T C 14.20% 27.93% T -> C NA
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g17200.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 4.595; most accessible tissue: Minghui63 panicle, score: 7.125
vg1109584748 (J) chr11 9584748 C T 50.90% 34.53% C -> T NA
LOC_Os11g17200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 4.595; most accessible tissue: Minghui63 panicle, score: 7.125
vg1109584772 (J) chr11 9584772 T C 1.60% 45.05% C -> T NA
LOC_Os11g17200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.073; most accessible tissue: Zhenshan97 flower, score: 9.663
vg1109584783 (J) chr11 9584783 C T 0.60% 52.35% C -> T NA
LOC_Os11g17200.1 Alt: T| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 5.073; most accessible tissue: Zhenshan97 flower, score: 9.663
vg1109585080 (J) chr11 9585080 C T 77.80% 18.15% C -> T NA
LOC_Os11g17200.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 8.049; most accessible tissue: Zhenshan97 flag leaf, score: 16.470
vg1109585099 (J) chr11 9585099 C Unkown 78.60% 18.09% C -> T NA
LOC_Os11g17200.1 Alt: T| missense_variant MODERATE(snpEff)
The average chromatin accessibility score: 8.049; most accessible tissue: Zhenshan97 flag leaf, score: 16.470
vg1109585481 (J) chr11 9585481 A G 77.40% 15.40% A -> G NA
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g17200.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 6.757; most accessible tissue: Minghui63 root, score: 13.235
vg1109585484 (J) chr11 9585484 A G 67.00% 5.54% G -> A NA
LOC_Os11g17200.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 6.757; most accessible tissue: Minghui63 root, score: 13.235
vg1109585503 (J) chr11 9585503 A G 72.30% 20.80% A -> G NA
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g17200.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 7.386; most accessible tissue: Minghui63 root, score: 13.235
vg1109585528 (J) chr11 9585528 A G 56.00% 24.35% G -> A NA
LOC_Os11g17200.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.386; most accessible tissue: Minghui63 root, score: 13.235
vg1109585537 (J) chr11 9585537 G A 70.40% 20.86% G -> A NA
LOC_Os11g17200.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.459; most accessible tissue: Minghui63 root, score: 13.235
vg1109585555 (J) chr11 9585555 C A 1.10% 48.20% C -> A NA
LOC_Os11g17200.1 Alt: A| stop_gained HIGH(snpEff)/stop_gained(CooVar)
LOC_Os11g17200.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 7.984; most accessible tissue: Minghui63 root, score: 13.235