Supplemental Material for O’Loughlin et al., 2021

Supplementary Table 1. MAF statistics. *The MAF is formatted as blocks of aligned sequences, with most blocks containing fewer than 21 genomes. This is the proportion of AgamP4 in the MAF that was aligned with all 21 genomes. **MAF containing aligned sequences of all 21 reference genomes.

Supplementary Figure 1. Total length of invariant bases within UCEs in non-overlapping 10kb windows across the Anopheles gambiae genome.

Supplementary Figure 2. Distribution of sizes of UCEs. Left panel: genic sequences; right panel intergenic sequences. Sequences containing any bases within a gene were treated as genic, all other sequences as intergenic. Supplementary Figure 3. Panther gene functional classification by GO-Slim terms. Top: molecular function; middle: biological process; bottom: cellular component. Left panel: genes containing UCEs; right panel: genes containing UCEs of length 50bp or over (for comparison with previous studies).

Supplementary Table 2. Sequences of Anopheles UCEs with coordinates from AgamP4 reference genome, genomic location and UCE length.

Supplementary Table 3. Anopheles gambiae genes containing UCEs, with no. of UCEs, no. of invariant sites within UCEs, gene descriptions, Drosophila orthologues and phenotypes.