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Table 1.

MHC capture and sequencing metrics

Sample ID	Sequencer	# SMRT cell per sample	Total sequenced reads	Reads passing quality filters	Reads used in pipeline	MHC-specific reads	% of MHC-specific reads	MHC-specific enrichment (fold)	Normalized MHC-specific reads
PGF + COX	Sequel II	0.5^a	966,185	553,336	553,336	98,975	17.89	149.06	82,327
EAS-F	Sequel II	0.5^b	1,051,700	595,848	595,848	271,760	45.61	380.07	97,567
EAS-M	Sequel II	0.5^a	1,432,295	799,875	600,000	315,453	52.58	438.13	111,471
EAS-P	Sequel II	1	4,834,630	1,912,901	600,000	172,559	28.76	239.67	117,112
AFA	Sequel II	0.5^b	1,106,650	637,925	600,000	178,484	29.75	247.89	97,500
EUR-F	Sequel	2	1,167,299	937,719	800,000	194,468	24.31	202.57	—^c
EUR-M	Sequel	3	2,008,996	1,586,392	1,586,392	163,881	10.33	86.09	—^c
EUR-P	Sequel	2	1,393,143	1,083,856	650,000	187,084	28.78	239.85	—^c

[i] Samples were sequenced on either the PacBio Sequel or Sequel II. All sequenced reads were processed with the CCS algorithm, retaining only HiFi reads for Sequel II samples, sub-HiFi reads were included for the Sequel samples (reads passing quality filters). The number of reads used in the pipeline (reads used in pipeline) depended on the sequencer and the percentage of MHC-specific reads (% MHC-specific reads) reflects the percent of all reads obtained that aligned to the MHC region. The maximum depth of coverage of the Sequel II samples was targeted to 250× using digital normalization (normalized MHC-specific reads).

[ii] (EAS-F) East-Asian father, (EAS-M) East-Asian mother, (EAS-P) East-Asian proband, (EUR-F) European father, (EUR-M) European mother, (EUR-P) European proband.

[iii] ^a,bThe higher capacity of the Sequel II allowed for multiple samples to be run together on a single flow cell, as indicated.

[iv] ^cMHC-specific reads in Sequel samples were not subjected to the digital normalization process due to the high error rate, so all MHC-specific reads were used in subsequent steps.