The references used for alignment were E. coli K12 substr. MG1655 (GenBank NC_000913.2), R. sphaeroides 2.4.1 with plasmids (GenBank AKVW01000000), P. falciparum 3D7 (GenBank GCA_000002765.1), and Human assembly 19/GRCh37 (GenBank GCA_000001405.1). The NA12878 diploid reference used to generate Table S2 in Additional file 3, Figure S1 in Additional file 4, and Figure S2 in Additional file 5 was created by the Gerstein Lab [37].
