Search for Variation by Gene:

Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
Upstream (kb, optional, must <= 10 kb) : Downstream (kb, optional, must <= 10 kb) :
Variations Type:

Optional: (The selected data will be displayed in the result page.)
 Show Gene Expression Atlas  Show Chromatin Accessibility Map
 Show Non-coding variation Scores

Search Results:

5 variations found. LOC_Os09g26330 (hypro1; putative; expressed), ranging from 15,914,089 bp to 15,915,028 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
vg0915914474 (J) chr09 15914474 G T 62.70% 0.00% T -> G NA
LOC_Os09g26330.1 Alt: G| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 82.868; most accessible tissue: Zhenshan97 panicle, score: 91.693
vg0915914855 (J) chr09 15914855 A ACCGCCG CCG 48.40% 0.02% ACCGCCGCCG -> A,ACCGCCGC CGCCG NA
LOC_Os09g26330.1 Alt: ACCGCCGCCGCCG| inframe_insertion MODERATE(snpEff)/inframe_variant(CooVar)
LOC_Os09g26330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g26330.1 Alt: A| disruptive_inframe_deletion MODERATE(snpEff)/inframe_variant(CooVar)
The average chromatin accessibility score: 85.245; most accessible tissue: Zhenshan97 panicle, score: 95.381
vg0915914947 (J) chr09 15914947 G A 51.30% 0.17% G -> A
mr1425 (All); LR P-value: 2.04E-06;
mr1904 (All); LR P-value: 2.21E-11;
mr1050_2 (All); LR P-value: 5.79E-10;
mr1272_2 (All); LR P-value: 1.93E-06;
mr1607_2 (All); LR P-value: 1.40E-07;
mr1904_2 (All); LR P-value: 5.19E-18;
mr1904_2 (Ind_All); LR P-value: 2.49E-07
LOC_Os09g26330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g26330.1 Alt: A| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
The average chromatin accessibility score: 87.564; most accessible tissue: Zhenshan97 panicle, score: 95.951
vg0915914957 (J) chr09 15914957 G A 52.00% 0.17% G -> A
mr1425 (All); LR P-value: 3.88E-06;
mr1482 (Ind_All); LR P-value: 4.61E-06;
mr1904_2 (All); LR P-value: 3.37E-16
LOC_Os09g26330.1 Alt: DEL/frameshift_variant(CooVar)
LOC_Os09g26330.1 Alt: A| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 86.954; most accessible tissue: Zhenshan97 panicle, score: 95.756
vg0915914968 (J) chr09 15914968 C G 52.10% 0.11% C -> G
mr1425 (All); LR P-value: 3.88E-06;
mr1482 (Ind_All); LR P-value: 4.61E-06;
mr1904_2 (All); LR P-value: 3.37E-16
LOC_Os09g26330.1 Alt: G| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)
LOC_Os09g26330.1 Alt: DEL/frameshift_variant(CooVar)
The average chromatin accessibility score: 86.857; most accessible tissue: Zhenshan97 panicle, score: 95.903