Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data

Table 1 Misalignment and multi-mapping reads in the combined reference

Data name	Species	Tissue	Cell count	Matching reference		Combined reference			Error in combined reference (%)
Data name	Species	Tissue	Cell count	Reads aligned to correct reference	Multi-mapping reads^a	Reads aligned to correct reference	Reads misaligned to other reference	Multi-mapping reads^a	Error in combined reference (%)
placentaD121	Human	Placenta	2522	35,877,521	1,499,012	35,828,222	11,252	1,665,421	0.50
liverP1	Human	Liver	957	3,179,327	329,018	3,165,784	3243	360,665	1.10
deciduaD12	Human	Decidua	1963	25,147,111	1,186,854	25,122,973	6205	1,333,260	0.61
10x_pbmc	Human	Peripheral blood mononuclear cells	9295	93,171,679	4,730,260	93,027,903	175,980	4,917,645	0.39
kidneyF41	Human	Kidney	3399	21,326,290	1,085,238	21,266,741	77,660	1,150,761	0.67
10x_hodgkin	Human	Hodgkin lymphoma	2502	19,341,273	891,978	19,305,209	22,330	990,901	0.63
10x_SCC	Human	Squamous cell carcinoma	4739	72,819,855	2,515,694	72,583,115	482,564	2,583,374	0.76
10x_lungcancer	Human	Lung cancer	4481	50,316,076	1,927,985	50,165,228	253,394	1,989,662	0.63
10x_adenocarcinoma	Human	Adenocarcinoma	3599	44,820,075	1,562,487	44,678,244	268,975	1,609,641	0.71
10x_NSCLC	Human	Non small cell lung cancer	6640	69,706,720	2,128,698	69,466,298	478,684	2,196,589	0.78
10x_mbrain	Mouse	Brain	8096	103,833,090	18,545,869	103,524,395	38,599	19,909,752	1.35
mcolonHC1	Mouse	Colon	1204	8,810,265	796,909	8,782,774	2440	903,531	1.24

^a"Multi-mapping reads" are not included in "Reads aligned to correct reference" or "Reads aligned to correct reference"

ISSN: 1471-2105