Table 1. Summary statistics for all samples, produced by SECAPR.

Reported for each sample (1. column) are the number of sequencing reads in the FASTQ sequencing files, before (2. column) and after (3. column) cleaning and trimming, the total count of assembled de novo contigs (4. column), the number of filtered contigs that matched target loci (5. column) and the number of sequencing reads that mapped to the new reference library generated from the contig MSAs during reference-based assembly (6. column). These summary statistics are automatically compiled and appended to a log file (summary_stats.txt) during different steps in the SECAPR pipeline.

Sample ID	FASTQ read pairs (raw)	FASTQ read pairs (cleaned)	Total contig count	Recovered target contigs	Reads on target regions
1087	291,089	276,072	277,628	562	22,308
1086	244,726	231,326	230,122	516	17,969
1140	206,106	192,676	153,377	469	18,039
1083	377,228	352,646	309,993	534	31,922
1082	277,999	262,378	258,359	556	19,491
1085	307,671	291,377	309,561	512	22,030
1079	315,801	298,450	306,369	550	13,969
1061	209,586	192,407	177,910	545	14,474
1068	295,402	278,069	264,865	563	22,013
1063	354,795	336,356	356,512	525	20,439
1080	459,485	434,951	433,954	531	41,068
1065	217,725	205,290	204,082	544	13,524
1073	302,798	286,021	289,612	529	15,598
1070	295,822	278,011	295,557	539	19,288
1064	408,723	384,908	405,080	543	21,531
1074	408,370	383,604	398,758	531	25,476
1166	405,667	385,442	410,292	544	29,697