Table 2. Characteristics of ShortBRED markers used to profile metagenomes and bacterial genomes.

	HMP	T2D	T2D_Short	Yatsunenko	Bacterial Genomes
Parameter settings
Clustering ID	8	8	8	8	8
Minimum marker length	85%	85%	85%	85%	85%
Average read BP	101	90	75	450	100
Min trusted BP	90	81	68	200	30
QM length	30	27	22	66	33
Statistics
Families after initial clustering	849	849	849	849	849
Families with true markers	820	820	820	**	820
Families without true markers	29	29	29	**	29
Total markers	4132	4135	4142	**	4132
True markers	4078	4078	4078	**	4078
Junction markers	48	50	61	**	48
Quasi markers	6	7	3	**	6
Dataset profiled
Samples profiled	82	272	91	107	3305

Legend: This table lists characteristics of the markers used to profile the metagenomes and bacterial genomes. Each metagenome from the Chinese cohort was profiled with one of two sets of markers (T2D and T2D_Short) corresponding to the two different read sizes used in the dataset (90 and 75 bp) None of the families without True Markers were combined in the second round of clustering.

** Centroids were used to profile the Yatsunenko dataset.