Reads statistics

Table 1. General statistics
Statistic	Description
Number of mapped reads	The total number of reads mapped to the reference genome.
Percent reads on target	The percentage of filtered reads mapped to any targeted region relative to all reads mapped to the reference. If no target regions file is specified, this value will be the percentage of reads passing uniquely mapped and/or non‑duplicate filters, or 100% if no filters were specified. A read is considered on target if at least one aligned base overlaps at least one target region. A read that overlaps a targeted region but where only flanking sequence is aligned, for example, due to poor matching of 5' bases of the read, is not counted.

Table 2. Amplicon read coverage statistics.
The following statistics describe the reads that are assigned to specific amplicons. Each sequence read is assigned to exactly one of the amplicons specified by the targets file. If a read spans multiple amplicon targets, the target region that the reads covers most is assigned. In the even of a tie, the target that is the closest to the 3' end is assigned.
Statistic	Description
Number of amplicons	The number of amplicons that is specified in the target regions file.
Percent assigned amplicon reads	The percentage of reads that were assigned to individual amplicons relative to all reads mapped to the reference. A read is assigned to a particular (inner) amplicon region if any aligned bases overlap that region. If a read might be associated with multiple amplicons, it is assigned to the amplicon region that has the greatest overlap of aligned sequence.
Average reads per amplicon	The average number of reads assigned to amplicons.
Uniformity of amplicon coverage	The percentage of amplicons that had at least 20% of the average number of reads per amplicon. Cumulative coverage is linearly interpolated between nearest integer read depth counts.
Amplicons with at least N reads	The percentage of all amplicons that had at least N reads.
Amplicons with no strand bias	The percentage of all amplicons that did not show a bias towards forward or reverse strand read alignments. An individual amplicon has read bias if it has ≥10 reads and the percentage of forward or reverse reads to total reads is greater than 70%. Amplicons with <10 reads are considered to have no strand bias.
Amplicons reading end-to-end	The percentage of all amplicons that were considered to have a sufficient proportion of assigned reads (70%) that covered the whole amplicon target from 'end‑to‑end'. To allow for error, the effective ends of the amplicon region for read alignment are within 2 bases of the actual ends of the region.
Amplicon base composition bias	A number that represents the proportion of amplicons showing low representation (<0.2x mean reads) in the lower and/or upper quartiles of amplicons ordered by increasing G/C base pair content of their insert sequences. The value is relative to that in the center 50th percentile of amplicons and weighted by the standard deviation of representation over all amplicons. An RMS (root mean square) value is used so that a bias greater in either upper or lower quartiles produces a larger value than a mean bias seen more equally in both outer quartiles. The value is 0 if the uniformity of amplicon coverage metric is 100%, however, the value is not necessarily high at lower amplicon uniformity.

Table 3. Target base coverage statistics.
The following statistics describe the targeted base reads of the reference. A base covered by multiple target regions is counted only once per sequencing read.
Statistic	Description
Bases in target regions	The total number of bases in all specified target regions of the reference.
Percent base reads on target	The percent of all bases covered by reads aligned to the reference that covered bases in target regions. Clipped bases, deletions, and insertions (relative to the reference) are not included in this percentage. If no specific target regions was specified, the targeted regions is the whole genome.
Average base coverage depth	The average number of reads of all targeted reference bases. This is the total number of base reads on target divided by the number of targeted bases, and therefore includes any bases that had no coverage.
Uniformity of base coverage	The percentage of bases in all targeted regions (or whole genome) that is covered by at least 20% of the average base coverage depth reads. Cumulative coverage is linearly interpolated between nearest integer base read depths.
Target base coverage at Nx	The percentage of target bases covered by at least N reads.
Target bases with no strand bias	The percentage of all target bases that did not show a bias toward forward or reverse strand read alignments. An individual target base is considered to have read bias if it has ≥10 reads and the percentage of forward or reverse reads to total reads is greater than 70%. Target bases with <10 reads are considered to have no strand bias.
Percent end‑to‑end reads	The percentage of on‑target reads that fully cover their assigned amplicon (insert) from 'end‑to‑end'. To allow for error, the effective ends of the amplicon region for read alignment are within 2 bases of the actual ends of the region.