Output

Output TSV file format

At the top of the file in the first row, there are two fields called "Total Number of Aligned Reads" and "Total Number of Mapped Genomes". They represent the total number of reads that are aligned and the total number of genomes to which those reads align from the given alignment file.

Columns in the TSV file:

1. Genome:
   This is the name of the genome found in the alignment file.
2. Final Guess:
   This represent the percentage of reads that are mapped to the genome in Column 1 (reads aligning to multiple genomes are assigned proportionally) after pathoscope reassignment is performed.
3. Final Best Hit:
   This represent the percentage of reads that are mapped to the genome in Column 1 after assigning each read uniquely to the genome with the highest score and after pathoscope reassignment is performed.
4. Final Best Hit Read Numbers:
   This represent the number of best hit reads that are mapped to the genome in Column 1 (may include a fraction when a read is aligned to multiple top hit genomes with the same highest score) and after pathoscope reassignment is performed.
5. Final high confidence hits:
   This represent the percentage of reads that are mapped to the genome in Column 1 with an alignment hit score of 50%-100% to this genome and after pathoscope reassignment is performed.
6. Final low confidence hits:
   This represent the percentage of reads that are mapped to the genome in Column 1 with an alignment hit score of 1%-50% to this genome and after pathoscope reassignment is performed.
7. Initial Guess:
   This represent the percentage of reads that are mapped to the genome in Column 1 (reads aligning to multiple genomes are assigned proportionally) before pathoscope reassignment is performed.
8. Initial Best Hit:
   This represent the percentage of reads that are mapped to the genome in Column 1 after assigning each read uniquely to the genome with the highest score and before pathoscope reassignment is performed.
9. Initial Best Hit Read Numbers:
   This represent the number of best hit reads that are mapped to the genome in Column 1 (may include a fraction when a read is aligned to multiple top hit genomes with the same highest score) and before pathoscope reassignment is performed.
10. Initial high confidence hits:
    This represent the percentage of reads that are mapped to the genome in Column 1 with an alignment hit score of 50%-100% to this genome and before pathoscope reassignment is performed.
11. Initial low confidence hits:
    This represent the percentage of reads that are mapped to the genome in Column 1 with an alignment hit score of 1%-50% to this genome and before pathoscope reassignment is performed.