Hi @isaacovercast and @dereneaton , I am running the denovo+reference pipeline, and I am getting some conflicting results. When I look at the s7 stats, I see that for some of my samples the number of refseq_mapped_reads is higher than the no. of reads_raw. Also, when I add the no. of refseq_mapped_reads and no. of refseq_unmapped_reads this is not equal (rather almost twice) to the no. of raw reads. I am interpreting the results wrong?? Also, to my surprise when using the denovo pipeline I am recovering more loci than when using reference+denovo. ANy thoughts on why the results I am getting are totally different to what I was expecting? THANKS!