Table S2.

Alternative bioinformatics pipeline metrics

Alternative workflow	USR1	USR2
Ion P1 Final ISPs (–min-read-length 30)	55,460,151	54,469,446
Ion P1 Total Bases (–min-read-length 30)	6.5 G	6.6 G
post-cutadapt Quality, Barcode, and Adapter Filtering	40,320,121	45,333,921
Mapped Reads to rCRS	13,206,569	7,563,075
Mapped Reads of 30–120bp, MAPQ ≥ 70	5,895,852	3,668,765
Mapped Reads post-Picard Tools Mark Duplicates	21,140	22,951
% relative to Final ISPs	0.04%	0.04%