MAF TBA genome alignment of reference assemblies from the An gambiae complex

Whole genome alignment of the of the reference assemblies from the members of the Anopheles gambiae species complex (AGC). The reference assemblies are mostly derived from colonized anopheline mosquitoes. This multiple genome alignment, in MAF format, include the new reference assemblies from six genomes of the AGC, plus the assemblies of An. gambiae PEST, An. gambiae Pimperena S, An. coluzzii, and two outgroup Pyretophorus species (An. christyi and An epiroticus). MAF for each chromosome arm are provided. See the SOM, section S1 for a full description of the methodology

VCF files of field individual samples from the AGC complex

This is a tar archive including the VCF files (one per chromosome arm) for the 69 individual mosquito samples sequenced at low-depth that passed QC filters, plus 2 outgroups (see SOM, section 2.2)

MAF genome alignment from HD field samples of An gambiae complex

Multiple whole genome alignments of the field individual samples from the members of the Anopheles gambiae species complex (AGC) sequenced at high depth. This multiple genome alignment, in MAF format, include the haploid genome of one individual sequenced at high depth in each six genomes of the AGC. The An gambiae PEST reference assembly and two outgroup Pyretophorus species (An christyi and An epiroticus) are also included. MAF for each chromosome arm are provided. See the SOM, section S2.1 and S3.1 for a full description of the methodology