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Search Results:

14 variations found. LOC_Os01g43440 (TOO MANY MOUTHS precursor; putative; expressed), ranging from 24,855,936 bp to 24,857,421 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
vg0124856043 (J) chr01 24856043 G T 99.70% 0.00% G -> T NA
LOC_Os01g43440.1 Alt: T| missense_variant MODERATE(snpEff)
LOC_Os01g43430.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g43450.1 Alt: T| upstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 94.209; most accessible tissue: Callus, score: 97.399
vg0124856227 (J) chr01 24856227 C G 73.80% 0.00% G -> C
mr1005 (All); LR P-value: 1.64E-09;
mr1133 (All); LR P-value: 1.99E-17;
mr1622 (All); LR P-value: 8.72E-07;
mr1830 (All); LR P-value: 1.99E-16;
mr1924 (All); LR P-value: 5.87E-13;
mr1019_2 (All); LR P-value: 3.32E-69;
mr1679_2 (All); LR P-value: 1.04E-20;
mr1771_2 (All); LR P-value: 6.16E-39;
mr1784_2 (All); LR P-value: 5.76E-45
LOC_Os01g43440.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 91.729; most accessible tissue: Zhenshan97 panicle, score: 95.654
vg0124856633 (J) chr01 24856633 G T 68.30% 0.57% G -> T NA
LOC_Os01g43440.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 85.784; most accessible tissue: Zhenshan97 panicle, score: 93.133
vg0124856754 (J) chr01 24856754 G A 95.50% 0.00% G -> A NA
LOC_Os01g43440.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 88.393; most accessible tissue: Zhenshan97 panicle, score: 93.657
vg0124856854 (J) chr01 24856854 C T 99.40% 0.00% C -> T NA
LOC_Os01g43440.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 87.834; most accessible tissue: Zhenshan97 panicle, score: 94.278
vg0124857038 (J) chr01 24857038 C T 93.60% 0.00% C -> T NA
LOC_Os01g43440.1 Alt: T| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.202; most accessible tissue: Zhenshan97 panicle, score: 95.016
vg0124857248 (J) chr01 24857248 G A 73.70% 0.00% A -> G
mr1005 (All); LR P-value: 4.27E-09;
mr1188 (All); LR P-value: 1.40E-10;
mr1575 (All); LR P-value: 3.16E-09;
mr1622 (All); LR P-value: 4.72E-07;
mr1830 (All); LR P-value: 8.24E-17;
mr1924 (All); LR P-value: 2.91E-13;
mr1679_2 (All); LR P-value: 3.63E-22;
mr1771_2 (All); LR P-value: 1.10E-39;
mr1784_2 (All); LR P-value: 5.60E-45
LOC_Os01g43440.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 90.648; most accessible tissue: Minghui63 panicle, score: 95.915
vg0124857349 (J) chr01 24857349 C T 95.50% 0.00% C -> T NA
LOC_Os01g43440.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.588; most accessible tissue: Minghui63 panicle, score: 96.161
vg0124857369 (J) chr01 24857369 ACGG A 99.40% 0.00% ACGG -> A NA
LOC_Os01g43440.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)
LOC_Os01g43450.1 Alt: A| upstream_gene_variant MODIFIER(snpEff)
LOC_Os01g43460.2 Alt: A| downstream_gene_variant MODIFIER(snpEff)
LOC_Os01g43460.1 Alt: A| downstream_gene_variant MODIFIER(snpEff)
The average chromatin accessibility score: 89.673; most accessible tissue: Minghui63 panicle, score: 96.113
vg0124857371 (J) chr01 24857371 G C 68.90% 0.40% G -> C
mr1751_2 (All); LR P-value: 1.42E-08;
mr1951_2 (Ind_All); LR P-value: 2.03E-06
LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os01g43440.1 Alt: C| synonymous_variant LOW(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.776; most accessible tissue: Minghui63 panicle, score: 96.113
vg0124857372 (J) chr01 24857372 G A 68.90% 0.40% G -> A NA
LOC_Os01g43440.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.771; most accessible tissue: Minghui63 panicle, score: 96.113
vg0124857381 (J) chr01 24857381 A G 43.20% 0.47% A -> G,ACCG NA
LOC_Os01g43440.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os01g43440.1 Alt: ACCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os01g43440.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 89.735; most accessible tissue: Minghui63 panicle, score: 96.207
vg0124857385 (J) chr01 24857385 C T 73.70% 0.00% T -> C
mr1005 (All); LR P-value: 1.90E-09;
mr1133 (All); LR P-value: 1.79E-17;
mr1622 (All); LR P-value: 6.51E-07;
mr1646 (All); LR P-value: 3.52E-06;
mr1830 (All); LR P-value: 1.64E-16;
mr1679_2 (All); LR P-value: 5.10E-21;
mr1771_2 (All); LR P-value: 3.97E-39;
mr1784_2 (All); LR P-value: 5.55E-45
LOC_Os01g43440.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 89.718; most accessible tissue: Minghui63 panicle, score: 96.207
STR0124857386 (J) chr01 24857386 CGCCGCC GCCG CGCCGCC GCCGCCG 67.60% 0.00% CGCCGCCGCC G -> CGCCGCCGCC GCCG NA