Table 1.

Overview of the read assignment accuracy of EAGLE-RC against the concatenation method with real datasets. The first part of the table provides details on each dataset such as the species of origin, the type of replication (biological or technical), the sequencing strategy and the divergence between the two progenitor species, represented by the two-way average nuclear identity (ANI). The sequencing strategy includes the sequencing layout (PE = paired-end, SE = single-end) followed by the read length in bp. The two-way ANI was obtained using the ANI calculator from [56] with default parameters. The ANI value for Mimulus could not be calculated because of excessive computation time requirements (> 6′000 CPU hours). The second part of the table shows the average number of uniquely mapped reads for each approach, which was used to calculate the average error rate on the third part of the table. The error rate was obtained by the number of reads assigned to the wrong genome divided by the total number of reads that were uniquely mapped and deduplicated

Datasets				Average number of uniquely mapped reads		Average error rate
Species	Type of replicate (#)	Sequencing layout and read length	Two-way average nuclear identity	Concatenated genome	Read classification	Concatenated genome	Read classification
Arabidopsis halleri	Biological (2)	PE150	94.29 ± 3.94%	17′258’758	18′311’330	3.98%	1.16%
Arabidopsis lyrata	Biological (2)	PE150		22′204’342	23′301’056	5.94%	1.45%
Mimulus guttatus	Technical (4)	SE150	N.A.	1′420’116	1′288’800	26.78%	7.52%
Mimulus luteus	Technical (4)	SE150		3′889’458	3′760’614	9.80%	2.29%
Gossypium arboreum	Technical (2)	PE125	91.07 ± 4.68%	253′912’667	254′261’702	0.0044%	0.0013%
Gossipyium raimondii	Technical (2)	PE125		242′590’069	246′935’598	0.0039%	0.0019%