MAQGene

MAQGene is a web-browser–based interface that streamlines identification of causal mutations from whole-genome sequencing (WGS) data in forward genetic screens. It was designed to make read-mapping and variant inspection accessible to wet-lab users by automatically running the MAQ (Mapping and Assembly with Quality) aligner on mutant sequencing reads and producing a customized, human-readable summary of sequence variants relative to a wild-type reference genome.

MAQGene supports single-end and paired-end mapping (reads up to 127 bp) and exposes alignment/interpretation parameters through a simple submission form with configurable defaults. Its primary output is a tabular variant report that can be readily converted to a spreadsheet for sorting, filtering, and cross-genome comparison (e.g., subtracting background variants). For each candidate variant, MAQGene reports coverage and quality-related metrics to help assess reliability and prioritizes likely functional changes using genome annotations (FASTA reference plus GFF exon features), labeling variants as intergenic/intronic or genic and, when applicable, as silent, missense, nonsense, or splice-site–affecting. The resulting ranked “priority list” facilitates rapid selection of candidates for validation (e.g., Sanger sequencing) and can be filtered to variants within a genetically mapped interval, enabling practical WGS-based mutant identification in systems such as C. elegans and, in principle, any organism with appropriate reference and annotation files.