## Average Base Quality

- Overall base average quality score and the average quality score of base with quality score >= Q30.
- 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 table contains the percentage of reads with a given average read quality.
- The plot is a histogram of average read quality.
- [_SUBSAMPLE-RATE_]% randomly sampled reads are used for this analysis.

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 table contains the percentage of reads with a given average read quality.
- The plot shows average quality at each base position/cycle.
- [_SUBSAMPLE-RATE_]% randomly sampled reads are used for this analysis.

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

- bbmerge 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

- Average and standard deviation of read GC.
- [_SUBSAMPLE-RATE_]% randomly sampled reads are used for this analysis.

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 strand.
- [_SUBSAMPLE-RATE_]% randomly sampled reads are used for this analysis.

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 2.68% randomly sampled reads are calculated using seal and reported in the table.
- Artifacts: Illumina sequencing artifacts and adapters not including DNA or RNA spike-in JGI Contaminants: Illumina sequencing adapters and artifacts and other various contaminants
- For "Artifacts (first 50bp)", The 1st 50bp (20bp for smRNA) of 2.68% randomly sampled reads are aligned to each other using seal.
- Non-synthetic Contaminants: prokaryotic and eukaryotic systematic contaminants
- Synthetic Contaminants: synthetic seqs used in library construction appearing as systematic contaminants
- Adapters: Illumina sequencing adapters Non-Synthetic Contaminants: common microbial contamination found in the sequencing process
- Additional info: Microbe Read Filtering: SOP 1077

Contaminant | Value | Contam DB Description | Path to DB
--- | --- | --- | ---
Artifacts | [_CONTAM-ART-SEA-PCT_]% | Sequencing artifacts | /global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/Illumina.artifacts.2013.12.no_DNA_RNA_spikeins.fa
[_CONTAN-ART-SEAL-FIRST-BP_]
DNA spike-ins | [_DNA-SPIKEIN-SEAL_PCT_]% | DNA spike-in sequences | /global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/DNA_spikeins.artifacts.2012.10.fa.bak
RNA spike-ins | [_RNA-SPIKEIN-SEAL_PCT_]% | RNA tru-seq spike-in sequences | /global/dna/shared/rqc/ref_databases/qaqc/databases/illumina.artifacts/RNA_spikeins.artifacts.2012.10.NoPolyA.fa
Fosmid | [_CONTAM-FOSMID-SEAL-PCT_]% | etc | /global/dna/shared/rqc/ref_databases/qaqc/databases/pCC1Fos.ref.fa
Mitochondria | [_CONTAM-MITO-SEAL-PCT_]% | etc | /global/dna/shared/rqc/ref_databases/ncbi/CURRENT/refseq.mitochondrion/refseq.mitochondrion
Chloroplast | [_CONTAM-CHLO-SEAL-PCT_]% | etc | /global/dna/shared/rqc/ref_databases/ncbi/CURRENT/refseq.plastid/refseq.plastid
PhiX | [_CONTAM-PHIX-SEAL-PCT_]% | etc | /global/dna/shared/rqc/ref_databases/qaqc/databases/phix174_ill.ref.fa
rRNA | [_CONTAM-RRNA-SEAL-PCT_]% | etc | /global/dna/shared/rqc/ref_databases/qaqc/databases/rRNA.fa
Non-synthetic Contaminants | [_CONTAM-NON-SYN-SEAL-PCT_]% | etc | /global/projectb/sandbox/gaag/bbtools/commonMicrobes/fusedERPBBmasked.fa.gz
Synthetic Contaminants | [_CONTAM-SYN-SEAL-PCT_]% | etc | /global/projectb/sandbox/gaag/bbtools/data/Illumina.artifacts.2013.12.no_DNA_RNA_spikeins.fa.gz
Adapters | [_CONTAM-ADAPTER-PCT_]% | etc | /global/projectb/sandbox/gaag/bbtools/data/adapters.fa

[_SKETCH-TABLE_]