Definition for the alignment metrics in output

[emattei]

Hi,
I was looking for the definitions of each of the alignment metrics that are output by chromap:
Number of reads
Number of mapped reads
Number of uniquely mapped reads
Number of reads have multi-mappings
Number of candidates
Number of mappings
Number of uni-mappings
Number of multi-mappings
Number of barcodes in whitelist
Number of corrected barcodes
uni-mappings
multi-mappings
total
Number of output mappings (passed filters)

Is there a place where they are described?
Thank you

[mourisl]

It is not described in the readme. This blog explored these alignment metrics: https://notarocketscientist.xyz/posts/2024-07-23-understanding-the-chromap-summary-file/, hope it is helpful.

[emattei]

That was helpful. I am still not 100% sure but I am going to paste it here so other people can find it easily:

• Number of reads: Total count of sequencing reads processed.
• Number of mapped reads: Reads successfully aligned to the reference genome.
• Number of uniquely mapped reads: Reads aligned to a single location in the genome.
• Number of reads with multi-mappings: Reads aligned to multiple locations in the genome.
• Number of candidates: Potential mapping locations considered during alignment.
• Number of mappings: Total successful alignments, including multiple mappings per read.
• Number of uni-mappings: Total alignments where reads map to a single location.
• Number of multi-mappings: Total alignments where reads map to multiple locations.
• Number of barcodes in whitelist: Barcodes matching the expected list of valid barcodes.
• Number of corrected barcodes: Barcodes adjusted to match valid entries in the whitelist.
• # uni-mappings: Number of fragments mapping to single location in the genome.
• # multi-mappings: Number of fragments mappig in multiple locations in the genome.
• Total: Sum of uni-mappings and multi-mappings.
• Number of output mappings (passed filters): Final count of fragments after deduplication and filtering.

If all the definitions seem correct feel free to close the issue.