Table 3.

Summary of QC metrics for each PBMC sample. A total of six PBMC datasets were analyzed with the SCTK-QC pipeline.

	GENCODE GRCh38 v27		GENCODE GRCh38 v34		SMART-Seq2
	PBMC1k V2	PBMC1k V3	PBMC1k V2	PBMC 1k V3	Replicate 1	Replicate 2
Total number of genes detected	58,347	60,669	58,347	60,669	33,694	33,694
Number of droplets, Droplet matrix	737,280	6,794,880	737,280	6,794,880	NA	NA
Number of Cells, Cell matrix	995	1223	996	1222	311	273
Mean counts	3559	7576	3553	7576	390,058	292,971
Median counts	3374	6637	3375	6640	388,420	290,819
Mean features detected	1133	2088	1140	2104	2436	2795
Median features detected	1106	1957	1109	1978	2406	2632
Scrublet, Number of doublets	12	16	12	18	0	3
Scrublet, Percentage of doublets	1.21	1.31	1.2	1.47	0	1.1
ScDblFinder, Number of doublets	13	16	14	20	3	13
ScDblFinder, Percentage of doublets	1.31	1.31	1.41	1.64	0.97	4.76
DoubletFinder, Number of doublets, Resolution 1.5	75	92	75	92	23	20
DoubletFinder, Percentage of doublets, Resolution 1.5	7.54	7.52	7.53	7.53	7.4	7.33
CXDS—Number of doublets	51	195	53	183	19	4
CXDS—Percentage of doublets	5.13	15.9	5.32	15	6.11	1.47
BCDS—Number of doublets	91	91	69	71	17	8
BCDS—Percentage of doublets	9.15	7.44	6.93	5.81	5.47	2.93
SCDS Hybrid—Number of doublets	65	119	77	90	20	13
SCDS Hybrid—Percentage of doublets	6.53	9.73	7.73	7.36	6.43	4.76
DecontX—Mean contamination percentage	5.4	3.7	5.8	3.0	2.1	2.9
DecontX—Median contamination percentage	1.7	0.9	1.8	0.7	0.7	1.3

A total of six PBMC datasets were analyzed with the SCTK-QC pipeline. Two GENCODE PBMC 1k datasets of differing 10x Chemistry were taken from GENCODE v27 and v34, resulting in a total of four datasets. Additionally, two SMART-Seq2 datasets from PBMC replicates were also taken. A per-sample summary table is automatically generated by the pipeline.