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Search Results:

7 variations found. LOC_Os11g09684 (expressed protein), ranging from 5,171,482 bp to 5,172,282 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
vg1105171877 (J) chr11 5171877 G C 84.10% 6.24% C -> G NA
LOC_Os11g09684.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09684.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.411; most accessible tissue: Minghui63 flag leaf, score: 98.105
vg1105171921 (J) chr11 5171921 A G 74.40% 5.82% A -> G NA
LOC_Os11g09684.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os11g09684.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 91.450; most accessible tissue: Minghui63 flag leaf, score: 98.001
vg1105172102 (J) chr11 5172102 C A 66.30% 6.22% C -> A
mr1128_2 (Ind_All); LR P-value: 8.43E-06;
mr1204_2 (Ind_All); LR P-value: 9.78E-06;
mr1376_2 (All); LR P-value: 2.39E-07;
mr1431_2 (All); LR P-value: 1.29E-07;
mr1538_2 (Ind_All); LR P-value: 7.10E-06;
mr1594_2 (Ind_All); LR P-value: 1.63E-06;
mr1624_2 (Ind_All); LR P-value: 7.50E-07;
mr1758_2 (Ind_All); LR P-value: 2.43E-08
LOC_Os11g09684.1 Alt: A| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.2 Alt: A| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09690.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 90.098; most accessible tissue: Minghui63 flag leaf, score: 95.773
vg1105172112 (J) chr11 5172112 G T 93.20% 5.67% G -> T NA
LOC_Os11g09684.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 90.259; most accessible tissue: Minghui63 flag leaf, score: 95.751
vg1105172211 (J) chr11 5172211 C T 93.50% 5.76% C -> T NA
LOC_Os11g09684.1 Alt: T| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.2 Alt: T| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09690.1 Alt: T| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
N Alt: DEL/silent_mutation(CooVar)
The average chromatin accessibility score: 88.736; most accessible tissue: Minghui63 flag leaf, score: 95.135
vg1105172215 (J) chr11 5172215 A G 93.60% 5.76% A -> G NA
N Alt: DEL/silent_mutation(CooVar)
LOC_Os11g09684.1 Alt: G| 3_prime_UTR_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.1 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09680.2 Alt: G| upstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
LOC_Os11g09690.1 Alt: G| downstream_gene_variant MODIFIER(snpEff)/silent_mutation(CooVar)
The average chromatin accessibility score: 88.513; most accessible tissue: Minghui63 flag leaf, score: 94.967
STR1105171917 (J) chr11 5171917 GGATACG GATACGC CAAT GGATGCG GATACGC CAAT 78.40% 0.00% GGATACGGAT ACGCCAAT -> GGATGCGGAT ACGCCAAT NA