Read QC analysis is generated by subsampling fastq to [_SUBSAMPLE-RATE_]% of the reads.
Average Base Quality, Average Read Quality, Read GC and Cycle Nucleotide Composition are generated by the BBTools reformat.sh command.

## Average Base Quality

- The table contains the percentage of bases with a given quality score.

Overall Base Quality Score: | [_BASE-QUALITY-SCORE_] ± [_BASE-QUALITY-SCORE-STD_]
Q30 Base Quality Score: | [_Q30-BASE-QUALITY-SCORE_] ± [_Q30-BASE-QUALITY-SCORE-STD_]

Quality Value Threshold | ≥Q30 | ≥Q25 | ≥Q20 | ≥Q15 | ≥Q10 | ≥Q5
--- | --- | --- | --- | --- | --- | ---
Count of Bases | [_COUNT-OF-BAESE-Q30_] | [_COUNT-OF-BAESE-Q25_] | [_COUNT-OF-BAESE-Q20_] | [_COUNT-OF-BAESE-Q15_] | [_COUNT-OF-BAESE-Q10_] | [_COUNT-OF-BAESE-Q5_]
Percentage % | [_PCT-OF-BAESE-Q30_] | [_PCT-OF-BAESE-Q25_] | [_PCT-OF-BAESE-Q20_] | [_PCT-OF-BAESE-Q15_] | [_PCT-OF-BAESE-Q10_] | [_PCT-OF-BAESE-Q5_]

## Average Read Quality

- The data file contains the percentage of reads with a given average read quality.
- The plot is a histogram of average read quality.

Quality Value Threshold | ≥Q30 | ≥Q25 | ≥Q20 | ≥Q15 | ≥Q10 | ≥Q5
--- | --- | --- | --- | --- | --- | ---
Percentage of Reads % | [_PCT-OF-READS-Q30_] | [_PCT-OF-READS-Q25_] | [_PCT-OF-READS-Q20_] | [_PCT-OF-READS-Q15_] | [_PCT-OF-READS-Q10_] | [_PCT-OF-READS-Q5_]

Average Read Quality Histogram ([_AVG-READ-QUAL-HISTO-DATA_], [_AVG-READ-QUAL-HOSTO-D3_] )

## Average Base Position Quality

- The data file contains the percentage of reads with a given average read quality.
- The plot shows average quality at each base position/cycle.

Q20 for Read 1: [_READ_Q20_READ1_]
Q20 for Read 2: [_READ_Q20_READ1_]

Average Base Position Quality Plot ( [_AVG-BASE-POS-QUAL-HISTO-DATA_], [_AVG-BASE-POS-QUAL-HISTO-D3_] )

## Insert Size

- BBTools bbmerge.sh is used to perform this analysis. bbmerge merges paired reads into single reads by overlap detection. With sufficient coverage, bbmerge can also merge nonoverlapping reads using gapped kmers.
- The "percentage reads joined" is calculated by (number of joined reads/total number of reads * 100).
- Raw reads are used for the insert size calculation (no trimming or filtering).

Insert Size Statistics

Percentage Reads Joined | Average | Stddev | Mode
--- | --- | --- | ---
[_PCT-READS-JOINED_] | [_PCT-READS-JOINED-AVG_] | [_PCT-READS-JOINED-STDDEV_] | [_PCT-READS-JOINED-MODE_]

Insert size histogram ( [_INSERT-SIZE-HISTO-DATA_], [_INSERT-SIZE-HISTO-D3_] )

## Read GC

- Histogram of GC percents for subsampled reads.

Average Read GC: [_READ-GC-AVG_] ± [_READ-GC-STDDEV_]%

Read GC Histogram ([_READ-QC-HISTO-DATA_], [_READ-QC-HISTO-D3_] )

## Cycle Nucleotide Composition

- The plot(s) show nucleotide counts at each cycle position.
- 1 plot is created for each read.

Read 1 Nucleotide Composition Frequency Plot ([_NUC-COMP-FREQ-R1-DATA_], [_NUC-COMP-FREQ-R1-D3_]) | Read 2 Nucleotide Composition Frequency Plot ([_NUC-COMP-FREQ-R2-DATA_], [_NUC-COMP-FREQ-R2-D3_])

## Percentage of Common Contaminants

- The percentage of common contaminants in the randomly sampled reads are calculated using BBTools seal.sh and reported in the table. Phix: PhiX control sequence.

Contaminant | Value | Contamination DB Description
--- | --- | ---
Artifacts | [_CONTAM-ART-SEA-PCT_]% | Illumina sequencing artifacts and adapters not including DNA or RNA spike-ins
[_CONTAN-ART-SEAL-FIRST-BP_]
DNA spike-ins | [_DNA-SPIKEIN-SEAL_PCT_]% | DNA spike-in sequences
RNA spike-ins | [_RNA-SPIKEIN-SEAL_PCT_]% | RNA spike-in sequences
Fosmid | [_CONTAM-FOSMID-SEAL-PCT_]% | fosmid sequences
Mitochondria | [_CONTAM-MITO-SEAL-PCT_]% | mitochondria sequences
Chloroplast | [_CONTAM-CHLO-SEAL-PCT_]% | chloroplast sequences
PhiX | [_CONTAM-PHIX-SEAL-PCT_]% | control sequences
rRNA | [_CONTAM-RRNA-SEAL-PCT_]% | ribosomal RNA sequences
Non-synthetic Contaminants | [_CONTAM-NON-SYN-SEAL-PCT_]% | common microbial contamination found in the sequencing process
Synthetic Contaminants | [_CONTAM-SYN-SEAL-PCT_]% | synthetic sequencess used in library construction appearing as systematic contaminants

[_SKETCH-TABLE_]