Extended Data Table 1. Imputation accuracy for C4 copy numbers in European ancestry and African American haplotypes.

Imputation accuracy was evaluated by correlation of imputation results to C4 gene copy numbers directly inferred from WGS data. Aggregated copy numbers imputed from each round of leaving 10 individuals out were correlated with the directly-typed measurements and are reported as r² for each feature of C4 structural variation for European ancestry and African American members of the reference panel separately.

	Imputation accuracy (r2)
Gene copy number	European ancestry	African Americans
C4	0.80	0.58
C4A	0.78	0.65
C4B	0.74	0.61
C4-HERV	0.91	0.76
2.3(C4A)+C4B	0.77	0.64