Hi! I hope you don't mind if I ask again. I would need a clarification about the final stats file in the outfiles folder. I run ipyrad as denovo-reference (chloroplast ref.) and when I look at those metrics I see that for example, for a sample, I have 805,763 raw reads, 801,554 passing filters, 4,841 mapping to the reference ("refseq_mapped_reads") but only 553,120 unmapped. So my question is: why mapped reads + unmapped reads is not equal to passing filters reads? From what I understand, using this assembly method, I would expect to discard the 4,841 reads mapping to the choloroplast sequence and used the 796,713 (801554-4841) remaining reads for the denovo assembly.