Lengths of pairwise shared haplotypes are greater between samples sharing a CNV allele than between wild-type samples. Shared haplotype lengths were calculated on either side of the CNV-containing region of the Cyp6aa/p gene cluster. Non-CNV (WT) samples were taken from the same populations as the focal CNV alleles. Bars show the distribution of shared haplotype lengths between all haplotype pairs with the same core haplotype. Bar limits show the interquartile range, fliers show the 5th and 95th percentiles, horizontal black lines show the median, and notches in the bars show the bootstrapped 95% confidence interval for the median. The names of the CNVs (Cyp6aap_Dup#) are abbreviated as Dup#: (BF) Burkina Faso; (CI) Côte d'Ivoire; (UG) Uganda; (col) An. coluzzii; (gam) An. gambiae.
