Hi,
Decreasing the value of the stat_q parameter will allow more markers to be considered when calculating relative abundances. You can also remove the filter on the MAPQ value by setting min_mapq_val to -1 so no reads are removed because of multiple mapping. There is another thread here https://forum.biobakery.org/t/understanding-parameters-stat-q-for-environmental-sample/2204 in which I explain what stat_q is.
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