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Gene ID/Symbol/Name (e.g., LOC_Os01g08570 or hwh1 or Os01g0180900 or gly%ltransferase, note: wildcard character '%' is also acceptable.):
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Search Results:

4 variations found. Os01g0839400/LOC_Os01g62220 (pentatricopeptide; putative; expressed), ranging from 36,011,649 bp to 36,013,020 bp (including 0 kb upstream and 0 kb downstream of the gene).

Gene IDAnnotation
LOC_Os01g62220 pentatricopeptide, putative; RAP ID: Os01g0839400; MSU ID: LOC_Os01g62220

Gene Expression Atlas:

The expression data is from the CREP database. And the expression value is log2-transformed. Move the mouse over the cells of the heat map to get detailed tissue information and expression values.

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
vg0136012413 (J) chr01 36012413 G T 87.30% 0.00% G -> T
mr1213 (Ind_All); LR P-value: 1.10E-07;
mr1887 (All); LR P-value: 6.95E-06;
mr1887 (Ind_All); LR P-value: 1.58E-06
LOC_Os01g62220.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/probably damaging(PolyPhen-2)
The average chromatin accessibility score: 72.981; most accessible tissue: Zhenshan97 panicle, score: 84.824
vg0136012464 (J) chr01 36012464 C T 66.70% 0.00% T -> C NA
LOC_Os01g62220.1 Alt: C| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/possibly damaging(PolyPhen-2)
The average chromatin accessibility score: 74.714; most accessible tissue: Callus, score: 86.839
vg0136012677 (J) chr01 36012677 T G 66.70% 0.00% G -> T NA
LOC_Os01g62220.1 Alt: T| missense_variant MODERATE(snpEff)/nonsynonymous_codon(CooVar)/benign(PolyPhen-2)
The average chromatin accessibility score: 73.473; most accessible tissue: Callus, score: 91.254
vg0136012918 (J) chr01 36012918 T C 97.90% 0.00% T -> C
mr1457_2 (Ind_All); LR P-value: 7.50E-06;
mr1458_2 (Ind_All); LR P-value: 7.00E-08
LOC_Os01g62220.1 Alt: C| synonymous_variant LOW(snpEff)/synonymous_codon(CooVar)
The average chromatin accessibility score: 63.678; most accessible tissue: Callus, score: 75.215