Average Base Quality

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