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.):
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Search Results:

30 variations found. LOC_Os06g41850 (SMP-30%2FGluconolaconase%2FLRE-like region containing protein; expressed), ranging from 25,093,241 bp to 25,094,294 bp (including 0 kb upstream and 0 kb downstream of the gene).

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

CategoryVariant IDChromPosGeneMSURAPAlt_Allele_FunctionRef_genoAlt_geno
Yield componentsvg0625093552Chr625093552TGW6LOC_Os06g41850Os06g0623700increasing grain weightCGC
Yield componentsvg0625093498Chr625093498TGW6LOC_Os06g41850Os06g0623700increasing grain weightCCGCTC

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: