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bmansfeld / QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
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difference between Upward peaks and Downward peaks ? #21

Closed qindan2008 closed 5 years ago

qindan2008 commented 5 years ago

Hi, When run QTLseqr, sometimes value of ∆(SNP-index) was positive, the peak was upward. But sometimes value of ∆(SNP-index) was negative, and the peak was downward.

So, how to interpret negative ∆(SNP-index) ？What is the biological significance?

Thank you very much.

bmansfeld commented 5 years ago

Hi, Positive delta SNP values indicate a qtl derived from the parent that isn't the reference. I negative peak represents qtl contributed by the reference parent. Hope this makes sense, Ben

qindan2008 commented 5 years ago

Does the reference parent refer to high bulk sample? The parent that isn't the reference refers to low bulk sample?

Thanks a lot.

bmansfeld commented 5 years ago

depends on your set up. I usually set the parent with the low bulk phenotype as the reference. That way the peaks with high delta SNP represent areas contributing to the alternate parent which has the high-bulk phenotype High peaks - high phenotype value makes sense in my head. Ben