plinkseq warning: serious incompatible REF sequences

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May 19, 2017, 4:23:38 AM5/19/17

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Dear All,

I am using your pseq to analyze some PLINK format data (bed/bim/fam). I got many warnings like

plinkseq warning: **serious** incompatible REF sequences : chr6:31375117

plinkseq warning: **serious** incompatible REF sequences : chr6:31377173

plinkseq warning: **serious** incompatible REF sequences : chr15:66792317

plinkseq warning: **serious** incompatible REF sequences : chr10:45958881

what this mean and what can I manage this case? If you can provide some code I will appreciate for it.

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