Table 2.

Summary of the MHC regional capture using dCATCH-Seq in three cell genomes

Cell	Conditiona	Total reads	Aligned reads	Alignment rate (%)	PCR duplicate rate (%)	Aligned reads on target	On-target rate (%)	Uniquely aligned reads on targetb	On-target rate (%)b
K562	With PCR	2,882,056	2,744,145	97.79	2.67	2,503,434	91.23	2,342,653	92.77
K562	Without PCR	1,922,388	1,795,403	97.67	4.43	1,633,616	90.99	1,528,150	92.71
GM12878	Without PCR	4,243,904	3,836,649	98.44	8.39	3,492,283	91.02	3,228,811	92.28
U937	Without PCR	1,489,332	1,244,031	95.96	13.63	1,033,606	83.09	983,376	86.38

^aConditions are defined based on with or without PCR amplification of DNA library after the first round of capture

^bUniqueness and relevant statistics are calculated from reads with MAPQ ≥20