Target sequence enrichment success before duplicate removal.

For each pool and sequence enrichment method this table details the total number of reads generated for the pool, the percentage of total reads mapped to the reference genome, the percentage of total reads mapped to the target regions, and the percentage of mapped reads that mapped to the target regions with mapping quality 20. The total number of reads for a pool is calculated from the fastq file(s) generated for each lane of sequencing. The percentage of reads mapped to the reference is calculated from the BAM file generated from merging all the Maq map files for each lane for a pool. The percentage of reads mapped to the target regions is calculated as the number of reads with at least one base overlapping a target region divided by the total number of reads. The percentage of reads mapped to the target regions with a mapping quality score Q20 is calculated as the number of reads with at least one base overlapping a target region with mapping Q20 divided by the total number of reads.a: Calculated by samtools view –c.b: Calculated by samtoools veiw -c -q 20.