Project Settings

The settings (alignment options, motif selection, and so on) for the project.

Trim Primer Log

Lists the read sorting results for all the amplicons.

Panel Primer Match Statistics

Lists the read sorting results for all the amplicons in a tab-separated values (*.tsv) format.

Analysis Log

Contains a summary of the alignment results in a standardized .json format.

Paired End Merge Report

Generated if Merge Pairs was selected for the project. Details how many reads were merged and how many reads could not be merged.

BAM/BAI

Contains the fully detailed alignment results.

Alignment Statistic Log

Contains a summary of the alignment results.

Consensus Sequence

Details the consensus sequence with the major alleles in FASTA format, where a major allele is defined as the allele with the highest frequency at a given position. All major alleles are reported unless the allele is the same as the reference.

Consensus Statistics

Lists the number of reads with each allele at each position in the sample.

Major Allele Report

Variant report for all major alleles.

Minor Allele Report

Variant report for all minor alleles, where a minor allele is defined as any other allele with a frequency that is less than the allele with the highest frequency at a given position.

Low Coverage Report

Lists all the regions with coverages that fell below the Total Coverage threshold that was specified for the project.

Motif

Lists all the motifs that were used for the project.

Amplicon

Lists all the amplicon regions that were used for the project along with the number of reads (forward, reverse, and total) per region.

Variants

A text file saved as <Sample Name>_variants.txt. The file details all the EMPOP variants for the project sample: Major, Minor, and Combined.