Mapping sequencing reads to reference genomes/genes

Deliverables are:

1. Nucleotide-by-nucleotide coverage of the reference sequence by original and trimmed (if requested) sequencing reads mapped to each strand of the reference sequence perfectly (without mismatches), as well as mapped with up to 1 mismatch (text or Excel 2007 file);

Additional deliverables are:

2. Sequencing Reads Quality Report (HTML document);

3. Table containing average number of reads mapped to each individual or both strands (customer defined) of the reference sequence perfectly as well as mapped with 1 mismatch, in a 500b moving window (or customer defined; text or Excel 2007 file);

4. Report containing automatically identified differences (SNPs, single nucleotide In/Dels, and long deletions) between reference sequence(s) and genomic material in sequenced sample (text or Excel 2007 file). Available only for 25+x average coverage of the reference genome(s) or by request;

5. Upon request, text file containing all reads not mapped to any of the reference sequences with up to 1 mismatch.