[{"_id":{"$oid":"601a75a0c9a338f09f238816"},"Sample":"lie50","Chromosome":"chr10","Position":{"$numberLong":"47663"},"Reference":"C","Mutation":"T","Run":"Run_test","SYMBOL":"TUBB8"},{"_id":{"$oid":"601a75a0c9a338f09f238817"},"Sample":"lie50","Chromosome":"chr10","Position":{"$numberLong":"47876"},"Reference":"T","Mutation":"C","Run":"Run_test","SYMBOL":"TUBB8"},{"_id":{"$oid":"601a75a0c9a338f09f238818"},"Sample":"lie50","Chromosome":"chr10","Position":{"$numberLong":"48005"},"Reference":"G","Mutation":"A","Run":"Run_test","SYMBOL":"TUBB8"},{"_id":{"$oid":"601a75a0c9a338f09f238819"},"Sample":"lie12","Chromosome":"chr10","Position":{"$numberLong":"48005"},"Reference":"G","Mutation":"A","Run":"Run_test","SYMBOL":"TUBB8"}]

db.collection.aggregate([{$group:{_id:{Chromosome:"$Chromosome",Position:"$Position",Reference:"$Reference",Mutation:"$Mutation"}}},{$count:"count"}])