. Author manuscript; available in PMC: 2023 Jun 1.

Published in final edited form as: Pharmacogenet Genomics. 2022 Feb 21;32(4):159–172. doi: 10.1097/FPC.0000000000000466

Table 2.

Summary of A2–6 discordance with A1 Amplicon Exon Sequencing calls in CYP2A6, CYP2A7 (exons 1–2), CYP2A13, and CYP2B6

Approach	# of samples	# of Genotyped Positions	Total Calls^a	Discordant Calls (vs. A1)^b	Discordance Rate (vs. A1)^b
A1 Amplicon Exon Sequencing (EUR+AFR)	1441^c	4789	6900949^c	N/A^d	N/A^d
A2 SNP Array (EUR)	935	6	5610	85	1.5%
A2 SNP Array (AFR)	506	15	7590	199	2.6%
A3 HRC Imputation (EUR)	935	49	45815	267	0.6%
A4 1000G Imputation (AFR)	506	172	87032	547	0.6%
A5 TOPMED Imputation (AFR)	506	160	80960	1040	1.3%
A6 Targeted Capture Sequencing (EUR)	209	4789	1000901	382	0.04%
A6 Targeted Capture Sequencing (AFR)	166	4789	794974	280	0.04%

^a.

Calculated by # of samples x # of genotyped positions

^b.

(see supplemental methods for details on calculations)

^c.

Within the 1441 samples (935 EUR and 506 AFR), 13601 variant calls were made. 13585 (99.9%) passed GQ≥20 (i.e. 99% or greater confidence in variant calls); all 13601 calls passed QUAL≥20

^d.

Not applicable, as A1 is the reference to which other approaches are compared

1000G: 1000 Genomes Project; AFR: African-ancestry individuals; EUR: European-ancestry individuals; GQ: Phred-scaled confidence that the genotype call is correct (GQ=20 indicates 99% confidence); HRC: Haplotype Reference Consortium; QUAL: Phred-scaled confidence that there is variation at the specified position (QUAL=20 indicates 99% confidence)