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23 variations found. LOC_Os08g41150 (MBTB30 - Bric-a-Brac; Tramtrack; Broad Complex BTB domain with Meprin and TRAF Homology MATH domain; expressed), ranging from 25,997,619 bp to 25,998,699 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
vg0825997634 (J) chr08 25997634 C T 99.90% 0.00% C -> T NA
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os08g41140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g41160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 61.450; most accessible tissue: Zhenshan97 panicle, score: 79.799
vg0825997637 (J) chr08 25997637 C T 64.50% 0.02% T -> C
mr1021 (All); LR P-value: 1.09E-20;
mr1323 (All); LR P-value: 3.36E-15;
mr1601 (All); LR P-value: 3.30E-37;
mr1689_2 (All); LR P-value: 3.22E-36
LOC_Os08g41150.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g41150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 61.458; most accessible tissue: Zhenshan97 panicle, score: 79.071
vg0825997714 (J) chr08 25997714 A G 99.90% 0.00% A -> G NA
LOC_Os08g41150.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os08g41140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g41160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 66.686; most accessible tissue: Zhenshan97 panicle, score: 82.888
vg0825997781 (J) chr08 25997781 G T 99.70% 0.00% G -> T NA
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 68.887; most accessible tissue: Zhenshan97 panicle, score: 85.254
vg0825997807 (J) chr08 25997807 G T 99.40% 0.00% G -> T,A NA
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
LOC_Os08g41150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 68.196; most accessible tissue: Zhenshan97 panicle, score: 84.374
vg0825997839 (J) chr08 25997839 CT C 98.80% 0.00% CT -> C NA
LOC_Os08g41150.1 Alt: C| frameshift_variant HIGH(snpEff)/frameshift_variant(CooVar)
The average chromatin accessibility score: 67.492; most accessible tissue: Zhenshan97 panicle, score: 84.824
vg0825997865 (J) chr08 25997865 T C 64.60% 0.02% C -> T
mr1021 (All); LR P-value: 6.32E-22;
mr1024 (All); LR P-value: 4.92E-26;
mr1323 (All); LR P-value: 8.77E-16;
mr1477 (All); LR P-value: 1.69E-20;
mr1601 (All); LR P-value: 2.22E-37;
mr1689_2 (All); LR P-value: 2.73E-38
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g41150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 70.712; most accessible tissue: Zhenshan97 panicle, score: 84.824
vg0825997874 (J) chr08 25997874 C T 91.50% 0.00% C -> T
mr1709_2 (All); LR P-value: 3.61E-13;
mr1709_2 (Ind_All); LR P-value: 2.33E-09
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 71.473; most accessible tissue: Zhenshan97 panicle, score: 84.824
vg0825998056 (J) chr08 25998056 GCCGTGG AGCCGAG GAGCTCC A G 94.30% 0.00% GCCGTGGAGC CGAGGAGCTC CA -> G NA
LOC_Os08g41150.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 74.959; most accessible tissue: Zhenshan97 panicle, score: 85.665
vg0825998059 (J) chr08 25998059 A G 58.90% 0.00% G -> A
mr1021 (All); LR P-value: 4.59E-21;
mr1024 (All); LR P-value: 1.07E-26;
mr1228 (All); LR P-value: 3.70E-15;
mr1323 (All); LR P-value: 1.03E-15;
mr1689_2 (All); LR P-value: 5.44E-39
LOC_Os08g41150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 75.267; most accessible tissue: Zhenshan97 panicle, score: 86.432
vg0825998064 (J) chr08 25998064 G C 99.70% 0.00% G -> C NA
LOC_Os08g41150.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 74.147; most accessible tissue: Zhenshan97 panicle, score: 86.058
vg0825998077 (J) chr08 25998077 G A 58.90% 0.00% A -> G
mr1021 (All); LR P-value: 4.59E-21;
mr1024 (All); LR P-value: 1.07E-26;
mr1228 (All); LR P-value: 3.70E-15;
mr1323 (All); LR P-value: 1.03E-15;
mr1689_2 (All); LR P-value: 5.44E-39
LOC_Os08g41150.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 71.485; most accessible tissue: Zhenshan97 panicle, score: 84.824
vg0825998133 (J) chr08 25998133 G A 64.70% 0.00% A -> G
mr1021 (All); LR P-value: 1.72E-21;
mr1024 (All); LR P-value: 2.34E-26;
mr1228 (All); LR P-value: 5.45E-15;
mr1323 (All); LR P-value: 5.07E-16;
mr1477 (All); LR P-value: 2.80E-20;
mr1601 (All); LR P-value: 2.12E-37;
mr1781 (All); LR P-value: 1.45E-06;
mr1689_2 (All); LR P-value: 7.07E-38
LOC_Os08g41150.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 71.124; most accessible tissue: Zhenshan97 panicle, score: 83.904
vg0825998164 (J) chr08 25998164 T A 45.90% 41.87% T -> A NA
LOC_Os08g41150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os08g41150.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 70.271; most accessible tissue: Zhenshan97 panicle, score: 83.904
vg0825998185 (J) chr08 25998185 C Unkown 70.30% 13.39% C -> G NA
LOC_Os08g41150.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os08g41140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g41160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 72.268; most accessible tissue: Zhenshan97 panicle, score: 83.410
vg0825998195 (J) chr08 25998195 C Unkown 90.50% 2.62% C -> T NA
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os08g41140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g41160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 71.960; most accessible tissue: Zhenshan97 panicle, score: 83.410
vg0825998334 (J) chr08 25998334 GCGATGC CATCCGA TGAAA G 99.90% 0.00% GCGATGCCAT CCGATGAAA -> G NA
LOC_Os08g41150.1 Alt: G| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os08g41140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g41160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 66.735; most accessible tissue: Minghui63 panicle, score: 77.956
vg0825998355 (J) chr08 25998355 A C 98.50% 0.00% A -> C NA
LOC_Os08g41150.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 66.260; most accessible tissue: Zhenshan97 panicle, score: 78.302
vg0825998465 (J) chr08 25998465 C G 99.90% 0.00% C -> G NA
LOC_Os08g41150.1 Alt: G| missense_variant MODERATE(snpEff)
LOC_Os08g41140.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g41160.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 55.350; most accessible tissue: Zhenshan97 young leaf, score: 65.804
vg0825998501 (J) chr08 25998501 G T 94.10% 0.00% G -> T NA
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 55.713; most accessible tissue: Zhenshan97 young leaf, score: 65.280
vg0825998516 (J) chr08 25998516 C A 99.60% 0.00% C -> A NA
LOC_Os08g41150.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 57.249; most accessible tissue: Zhenshan97 young leaf, score: 66.320
vg0825998657 (J) chr08 25998657 C T 99.90% 0.00% C -> T NA
LOC_Os08g41150.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os08g41140.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
LOC_Os08g41160.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 39.363; most accessible tissue: Zhenshan97 young leaf, score: 48.658
vg0825998666 (J) chr08 25998666 C T 64.50% 0.00% T -> C
mr1021 (All); LR P-value: 6.32E-22;
mr1024 (All); LR P-value: 4.92E-26;
mr1323 (All); LR P-value: 8.77E-16;
mr1477 (All); LR P-value: 1.69E-20;
mr1601 (All); LR P-value: 2.22E-37;
mr1689_2 (All); LR P-value: 2.73E-38
LOC_Os08g41150.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 39.217; most accessible tissue: Zhenshan97 young leaf, score: 47.986