qa output formats

The qa command can produce the following outputs, selected with -o, --out_format. Results are printed to the console, or to a file with -f. Formats 1, 2, and 3 are printed as a table formatted for console output unless --tab_table is given, in which case a tab-separated values table is produced. Formats 4 to 8 are always printed as tab-separated text, and format 9 is a FASTA file. The statistics are described in Reported statistics.

  1. Summary of bin completeness, contamination, and strain heterogeneity: Bin Id, Marker lineage, # genomes, # markers, # marker sets, 0-5+, Completeness, Contamination, and Strain heterogeneity.

  2. Extended summary of bin quality: the statistics of format 1 along with genome statistics (e.g., GC, genome size, coding density). Coverage information is appended when a coverage file is given with -c.

  3. Summary of bin quality for increasingly basal lineage-specific marker sets: as format 1, with each lineage-specific marker set considered for the bin on a separate row.

    • Node Id: unique ID of the internal node in the genome tree from which lineage-specific markers were inferred

  4. List of marker genes for each bin along with the number of times each marker was identified:

    • Node Id: unique ID of the internal node in the genome tree from which lineage-specific markers were inferred

    • Marker lineage: indicates the lineage used for inferring the marker set

    • Useful for identifying lineage-specific gene loss or duplication.

  5. List of bin ID, marker gene ID, and called gene ID for each identified marker gene.

  6. List of marker genes present multiple times in a bin.

  7. List of marker genes present multiple times on the same scaffold.

    • Useful for identifying true gene duplication events, gene calling errors, or assembly errors. See the note on adjacent marker genes in qa.

  8. List indicating the position of each marker gene within a bin.

  9. FASTA file of marker genes identified in each bin. The header of each sequence gives the bin ID, the contig, the gene (geneId, start, end, strand, protlen), and the marker hit (marker, mstart, mend). Do not use --tab_table with this format, as only the FASTA output is supported.