Sequencing summary
Measure	Standalone 16S rRNA gene sequencing		Combined 16S rRNA gene + ITS sequencing
	HiSeq (bac)	**HiSeq (fungi)	MiSeq (bac)	MiSeq (fungi)
Raw input read counts	54,292 (4,604 - 209,300)	54,292 (4,604 - 209,300)	120,472 (66,686 - 166,697)	120,472 (66,686 - 166,697)
*Filtered & separated read counts	53,098 (4,448 - 205,205)	780 (89 - 2,634)	38,321 (9,778 - 86,404)	82,504 (35,342 - 130,199)
% average reads (range)	98 (96 - 98)	1 (1 - 2)	32 (9 - 61)	68 (40 - 91)
dada2 output read counts	45,793 (3,812 - 170,976)	NA	27,809 (6,246 - 55,428)	54,931 (5,211 - 106,289)
Succesfully aligned reads (BLAST)	45,786 (3,812 - 170,839)	NA	25,157 (4,470 - 54,899)	8,083 (144 - 55,944)
Filtered & verified reads (taxminer)	45,768 (3,812 - 170,832)	NA	25,044 (4,370 - 54,752)	5,834 (0 - 55,623)
* The reads containing ambiguous bases (Ns) were removed before the library split.
** No PCR-amplification for ITS; likely reflecting cross-reactivity of 16S rRNA gene primers with 18S rRNA gene region upstream of ITS1.