Number of mapped reads

Total number of reads mapped to the reference.

Number of reads on target

Total number of reads mapped to any targeted region of the reference. A read is considered to be on target if at least one aligned base overlaps a 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.

Target Base Coverage

Summary statistics for targeted base reads of the reference. A base covered by multiple target regions is only counted once per sequencing read.

Bases in target regions

The total number of bases in all specified target regions of the reference.

Percent of reads on target

The percentage of reads mapped to any targeted region relative to all reads mapped to the reference.

Total aligned base reads

The total number of bases covered by reads aligned to the reference.

Total base reads on target

The total number of target bases covered by any number of aligned reads.

Percent base reads on target

The percent of all bases covered by reads aligned to the reference that covered bases in target regions.

Bases in targeted reference

The total number of bases in all target regions of the reference.

Bases covered (at least 1x)

The total number of target bases that had at least one read aligned over the proximal sequence. Only the aligned parts of each read are considered. For example, unaligned (soft-cut) bases at the 5' ends of mapped reads are not considered. Covered target reference bases may include sample DNA read base mismatches, but does not include read base deletions in the read, nor insertions between reference bases.

Average base coverage depth

The average number of reads of all targeted reference bases.

Uniformity of base coverage

The percentage of bases in all targeted regions (or whole genome) covered by at least 0.2x the average base coverage depth.

Average base read depth

The average number of reads of all targeted reference bases that were read at least once.

Genome Base Coverage

Summary statistics for base reads of the reference genome.

Genome base coverage at N x

The percentage of reference genome bases covered by at least N reads.

Target coverage at N x

The percentage of target bases covered by at least N reads.

Targets with no strand bias

The percentage of all targets that did not show a bias towards forward or reverse strand read alignments. An individual target is considered to have read bias if it has at least 10 reads and the fraction of forward or reverse reads to total reads is greater than 70%.

Amplicon Read Coverage

Summary statistics for reads assigned to specific amplicons.Each sequence read will be assigned to exactly one of the amplicons specified by the targets file.Reads are assigned to particular amplicon targets based if their (5') mapping location being sufficientlyclose to the end of the amplicon region, taking the read direction (mapping strand) in to account.

Number of amplicons

The number of amplicons specified in the target regions file.

Percent assigned amplicon reads

The total number of reads that were assigned to individual amplicons.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 this way 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 bases in all targeted regions (or whole genome) covered by at least 0.2x the average base read depth.

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 strandread alignments. An individual amplicon is considered to have read bias if it has at least 10reads and the fraction of forward or reverse reads to total reads is greater than 70%.

Amplicons reading end-to-end

The percentage of all amplicons that were considered to have a sufficient proportion ofassigned reads (70%) that covered the whole amplicon target from 'end-to-end'. To allow for errorthe effective ends of the amplicon region for read alignment are within 2 bases of the actualends of the region.

Amplicon based composition bias

A number that represents the proportion of amplicons showing low representation (<.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.