FQreport is a command line program written in C++ for estimating several standard descriptive statistics from FASTQ-formatted High-Throughput Sequencing (HTS) read files:
▹ numbers of HTS reads and bases,
▹ distribution of HTS read lengths,
▹ nucleotide residue content per HTS read position,
▹ distribution of Phred scores (Ewing and Green 1998), and corresponding quartiles,
▹ distribution of Phred scores per HTS read position, and corresponding quartiles,
▹ distribution of the average Phred score per HTS read, and corresponding quartiles,
▹ distribution of the number of sequencing error(s) per HTS read (Edgar and Flyvbjerg 2015), and corresponding quartiles.
FQreport is the C++ re-implementation of the core part of the tool fastq_info, initially written in AWK (up to fastq_info v2.0).
Run FQreport with option -h to read the following documentation:
FQreport
USAGE: fqreport [-i <infile>] [-o <outfile>] [-f <name>] [-p <offset>] [-h]
OPTIONS:
-i <file> input file in FASTQ format (default: standard input)
-f <string> sample name (default: file name set using option -i)
-o <file> output file name (default: standard output)
-p <33|64> Phred offset (default: 33)
-h print this help and exit
EXAMPLES:
fqreport -i infile.fastq -o report.txt
fqreport -i infile.fastq -f sample -p 64
cat infile.fastq | fqreport -f sample -o report.txt
gunzip -c infile.fastq.gz | fqreportInput FASTQ file can be either specified using option -i (i.e. uncompressed file) or read via standard input (i.e. uncompressed data). Output results are written into standard ouput, but can be written into a specified output file using option -o.
The four first lines of the output results are the input file name (that can be modified using option -f), the total numbers of sequenced HTS reads (NR) and bases (NB), and the average HTS read length (AL). Next, a table is displayed with row number (column n) varying from 0 to the maximum HTS read length. For each value n, different descriptive statistics are ouputted: percentage of HTS read of length n (column Lfreq), base frequencies at position n (columns pA, pC, pG, pT, pN), percentage of HTS read with n expected sequencing error(s) (column Efreq), quartiles of the Phred scores at position n (columns Q1, Q2, Q3), and Phred score frequencies at position n for Q varying from 0 to the maximum observed value. Finally, the output table displays three last descriptive statistics for the whole FASTQ file: the Phred score frequencies (raw all.Phred(B)), the frequencies of average Phred score per HTS read (raw avg.Phred(R)), and the frequencies of expected sequencing error(s) per HTS read (row no.Errors(E)).
In the outputted table, every empty entry is indicated by a dot instead of zero.
To edit the descriptive statistics computed by FQreport using a spreadsheet program, the outputted table can be easily converted into tab-delimited format, e.g.fqreport -i infile.fastq | tr -d '#:' | sed '/--/d;s/Q= /Q=/g;s/ \+/\t/g;s/\t\./\t/g' > output.tsv
You can also use the tool fastq_info that supplements FQreport to deal with compressed FASTQ files and to obtain several ouputs (e.g. reduced table, tab-delimited summary, graphical representations).
The following Bash command line enables to download the pair of gzipped FASTQ files SRR001666_1.fastq.gz and SRR001666_2.fastq.gz to be used as examples:
wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR001/SRR001666/SRR001666*.fastq.gzThe following command line runs FQreport to analyze the second (i.e. R2) downloaded file:
gunzip -c SRR001666_2.fastq.gz | fqreport -f SRR001666_2leading to the following standard output in few seconds:
##File: SRR001666_2
#no.reads(NR): 7047668
#no.bases(NB): 253716048
#avg.lgt(AL): 36.0
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
n Lfreq pA pC pG pT pN Efreq Q1 Q2 Q3 Q= 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
----- ------ ------ ------ ------ ------ ------ ------ -- -- -- ------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
0 . . . . . . 47.10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1 . 27.43 24.14 23.31 25.03 0.09 26.29 40 40 40 0.1 0.0 0.0 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 94.2
2 . 27.21 23.34 23.77 25.55 0.13 12.44 40 40 40 0.1 0.0 0.0 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 94.2
3 . 25.58 24.88 24.19 25.17 0.18 5.93 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 92.3
4 . 24.62 25.17 25.17 24.82 0.22 3.01 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 92.3
5 . 24.87 24.22 25.59 25.11 0.21 1.67 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.3 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 91.5
6 . 24.69 25.45 25.39 24.23 0.25 1.00 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.3 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.4 90.6
7 . 24.83 24.49 25.80 24.67 0.21 0.65 40 40 40 0.2 0.1 0.0 0.1 0.2 0.2 0.1 0.1 0.1 0.2 0.4 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 87.4
8 . 24.93 25.01 25.05 24.81 0.21 0.44 40 40 40 0.2 0.1 0.0 0.1 0.2 0.2 0.1 0.1 0.1 0.2 0.4 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 86.8
9 . 24.43 25.32 25.25 24.77 0.23 0.32 40 40 40 0.2 0.1 0.1 0.1 0.2 0.3 0.2 0.2 0.2 0.2 0.5 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.7 82.7
10 . 24.83 25.13 25.50 24.30 0.25 0.24 40 40 40 0.2 0.1 0.1 0.1 0.3 0.3 0.2 0.2 0.2 0.2 0.6 0.3 0.3 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.8 0.8 0.8 80.5
11 . 24.67 25.24 25.32 24.50 0.26 0.18 40 40 40 0.3 0.1 0.1 0.2 0.3 0.3 0.2 0.2 0.2 0.3 0.6 0.3 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 78.6
12 . 24.43 25.55 25.42 24.38 0.21 0.14 39 40 40 0.2 0.1 0.1 0.2 0.3 0.4 0.2 0.3 0.3 0.3 0.8 0.4 0.5 0.5 0.5 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.8 0.8 0.8 0.8 0.8 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 1.0 1.0 74.4
13 . 24.68 25.31 25.39 24.36 0.25 0.11 35 40 40 0.3 0.2 0.1 0.2 0.3 0.4 0.3 0.3 0.3 0.4 0.8 0.5 0.5 0.6 0.6 0.7 0.7 0.7 0.8 0.8 0.8 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.0 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 70.0
14 . 24.62 25.33 25.30 24.50 0.26 0.09 33 40 40 0.3 0.2 0.1 0.2 0.4 0.5 0.3 0.3 0.4 0.4 0.9 0.5 0.6 0.6 0.7 0.7 0.8 0.8 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.2 1.2 1.1 1.1 1.1 1.1 1.1 67.8
15 . 24.36 25.64 25.36 24.40 0.24 0.07 31 40 40 0.2 0.2 0.1 0.2 0.4 0.5 0.3 0.4 0.4 0.5 1.1 0.6 0.7 0.7 0.8 0.8 0.9 0.9 1.0 1.0 1.0 1.1 1.1 1.1 1.1 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 64.8
16 . 24.51 25.49 25.45 24.31 0.24 0.05 28 40 40 0.2 0.3 0.1 0.3 0.5 0.7 0.4 0.5 0.5 0.6 1.3 0.8 0.8 0.9 0.9 1.0 1.0 1.1 1.1 1.2 1.2 1.2 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.2 59.8
17 . 24.43 25.61 25.37 24.39 0.21 0.04 25 40 40 0.2 0.3 0.2 0.3 0.6 0.8 0.5 0.5 0.6 0.7 1.6 0.9 1.0 1.1 1.1 1.2 1.2 1.3 1.3 1.4 1.4 1.4 1.4 1.4 1.5 1.5 1.5 1.5 1.5 1.5 1.4 1.4 1.4 1.4 1.4 1.4 1.4 1.3 1.3 1.3 54.9
18 . 24.19 25.75 25.42 24.25 0.40 0.02 24 40 40 0.4 0.3 0.2 0.4 0.6 0.8 0.5 0.6 0.7 0.7 1.7 1.0 1.1 1.2 1.2 1.3 1.3 1.4 1.4 1.5 1.5 1.5 1.5 1.5 1.5 1.6 1.6 1.6 1.5 1.5 1.5 1.5 1.5 1.5 1.4 1.4 1.4 1.4 1.3 1.3 52.2
19 . 24.37 25.64 25.53 24.22 0.24 0.01 22 39 40 0.2 0.3 0.2 0.4 0.7 1.0 0.6 0.7 0.8 0.9 2.0 1.1 1.2 1.3 1.4 1.4 1.5 1.5 1.6 1.6 1.6 1.6 1.7 1.7 1.7 1.7 1.7 1.6 1.6 1.6 1.6 1.6 1.5 1.5 1.5 1.4 1.4 1.4 1.3 1.3 48.8
20 . 24.27 25.68 25.46 24.34 0.25 0.01 20 35 40 0.3 0.4 0.2 0.5 0.9 1.2 0.7 0.8 0.9 1.0 2.4 1.3 1.4 1.5 1.6 1.6 1.7 1.7 1.8 1.8 1.8 1.8 1.8 1.8 1.8 1.8 1.8 1.7 1.7 1.7 1.6 1.6 1.6 1.5 1.5 1.4 1.4 1.4 1.3 1.3 43.9
21 . 24.06 25.88 25.51 24.26 0.29 0.01 19 33 40 0.3 0.5 0.3 0.6 1.0 1.3 0.8 0.9 1.0 1.1 2.6 1.5 1.6 1.7 1.7 1.8 1.8 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.8 1.8 1.8 1.8 1.7 1.7 1.6 1.6 1.5 1.5 1.4 1.4 1.4 1.3 1.3 40.7
22 . 24.25 25.71 25.59 24.21 0.25 0.01 18 31 40 0.3 0.5 0.3 0.7 1.1 1.4 0.9 1.0 1.2 1.3 3.0 1.7 1.7 1.8 1.9 2.0 2.0 2.0 2.1 2.1 2.1 2.0 2.0 2.0 2.0 1.9 1.9 1.8 1.8 1.7 1.7 1.6 1.6 1.5 1.5 1.4 1.4 1.3 1.3 1.2 37.3
23 . 24.26 25.66 25.44 24.35 0.29 0.01 16 28 40 0.3 0.6 0.4 0.8 1.3 1.7 1.0 1.2 1.3 1.5 3.4 1.9 2.0 2.1 2.1 2.2 2.2 2.2 2.2 2.2 2.2 2.2 2.1 2.1 2.0 2.0 1.9 1.9 1.8 1.7 1.7 1.6 1.6 1.5 1.4 1.4 1.3 1.3 1.2 1.2 33.3
24 . 24.11 25.85 25.54 24.24 0.26 0.01 15 26 40 0.3 0.7 0.4 0.9 1.4 1.9 1.2 1.4 1.6 1.7 3.9 2.1 2.3 2.3 2.4 2.4 2.4 2.4 2.4 2.4 2.3 2.3 2.2 2.2 2.1 2.0 1.9 1.9 1.8 1.7 1.6 1.6 1.5 1.4 1.4 1.3 1.3 1.2 1.1 1.1 29.4
25 . 24.21 25.82 25.59 24.16 0.21 0.01 13 24 40 0.2 0.9 0.5 1.0 1.7 2.3 1.4 1.6 1.8 2.0 4.4 2.4 2.5 2.5 2.6 2.6 2.6 2.6 2.5 2.5 2.4 2.3 2.3 2.2 2.1 2.0 1.9 1.8 1.8 1.7 1.6 1.5 1.5 1.4 1.3 1.2 1.2 1.1 1.1 1.0 26.0
26 . 24.13 25.89 25.45 24.33 0.20 0.01 12 22 38 0.2 1.0 0.6 1.2 2.0 2.6 1.6 1.8 2.0 2.2 4.9 2.6 2.7 2.7 2.7 2.7 2.7 2.7 2.6 2.5 2.4 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 1.5 1.4 1.3 1.2 1.2 1.1 1.1 1.0 1.0 23.4
27 . 23.94 26.03 25.60 24.24 0.20 0.01 12 21 36 0.2 1.2 0.7 1.4 2.2 2.9 1.8 2.0 2.2 2.4 5.2 2.8 2.8 2.9 2.8 2.8 2.8 2.7 2.6 2.5 2.5 2.4 2.3 2.1 2.0 1.9 1.8 1.8 1.6 1.6 1.5 1.4 1.3 1.3 1.2 1.1 1.1 1.0 0.9 0.9 21.3
28 . 24.04 25.94 25.60 24.20 0.22 0.01 11 19 33 0.2 1.4 0.8 1.6 2.5 3.3 2.0 2.2 2.4 2.6 5.7 3.0 3.0 3.0 3.0 2.9 2.9 2.8 2.7 2.6 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.2 1.2 1.1 1.0 1.0 0.9 0.9 0.8 19.0
29 . 23.90 25.77 25.47 24.42 0.43 0.01 10 18 31 0.4 1.6 0.9 1.8 2.8 3.6 2.2 2.4 2.6 2.8 6.0 3.1 3.1 3.1 3.1 3.0 2.9 2.8 2.7 2.6 2.4 2.3 2.2 2.1 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.3 1.2 1.1 1.0 1.0 0.9 0.9 0.8 0.8 17.3
30 . 23.68 26.19 25.54 24.32 0.28 0.01 10 17 29 0.3 1.8 1.1 2.1 3.2 4.1 2.4 2.7 2.9 3.1 6.4 3.3 3.3 3.2 3.1 3.0 2.9 2.8 2.7 2.5 2.4 2.2 2.1 2.0 1.8 1.7 1.6 1.5 1.4 1.3 1.3 1.2 1.1 1.0 1.0 0.9 0.8 0.8 0.8 0.7 15.4
31 . 23.72 25.93 25.52 24.58 0.25 0.01 9 16 28 0.2 2.1 1.3 2.4 3.5 4.6 2.7 2.9 3.1 3.3 6.8 3.4 3.4 3.3 3.2 3.0 2.9 2.8 2.6 2.5 2.3 2.2 2.0 1.9 1.8 1.6 1.5 1.4 1.3 1.3 1.2 1.1 1.0 1.0 0.9 0.8 0.8 0.7 0.7 0.7 13.8
32 . 23.66 25.83 25.41 24.84 0.26 0.01 9 15 26 0.3 2.5 1.5 2.6 3.9 5.0 2.9 3.1 3.3 3.4 7.1 3.5 3.4 3.3 3.2 3.1 2.9 2.7 2.6 2.4 2.2 2.1 1.9 1.8 1.7 1.6 1.4 1.3 1.2 1.2 1.1 1.0 0.9 0.9 0.8 0.8 0.7 0.7 0.6 0.6 12.6
33 . 23.39 26.10 25.53 24.78 0.21 0.01 8 14 24 0.2 2.9 1.7 3.0 4.4 5.5 3.1 3.4 3.5 3.6 7.4 3.6 3.5 3.4 3.2 3.0 2.9 2.7 2.5 2.3 2.2 2.0 1.9 1.7 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.9 0.8 0.8 0.7 0.7 0.6 0.6 0.5 11.0
34 . 23.37 26.10 25.54 24.78 0.21 0.02 7 13 23 0.2 3.3 1.9 3.3 4.8 6.0 3.4 3.6 3.8 3.8 7.6 3.7 3.6 3.4 3.2 3.0 2.8 2.6 2.4 2.2 2.1 1.9 1.8 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.9 0.8 0.7 0.7 0.6 0.6 0.6 0.5 0.5 9.7
35 . 23.22 25.87 25.63 25.02 0.26 0.04 6 12 22 0.3 3.9 2.2 3.7 5.2 6.4 3.6 3.8 3.9 4.0 7.8 3.7 3.6 3.4 3.2 2.9 2.7 2.5 2.3 2.1 2.0 1.8 1.7 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.9 0.8 0.7 0.7 0.6 0.6 0.6 0.5 0.5 0.5 8.8
36 100.00 22.91 25.92 25.70 25.26 0.22 0.06 6 12 21 0.2 4.2 2.3 4.0 5.5 6.6 3.7 3.8 3.9 3.9 7.6 3.6 3.5 3.3 3.0 2.8 2.6 2.4 2.2 2.1 1.9 1.7 1.6 1.5 1.3 1.2 1.1 1.1 1.0 0.9 0.8 0.8 0.7 0.7 0.6 0.6 0.5 0.5 0.5 0.4 9.0
----- ------ ------ ------ ------ ------ ------ ------ -- -- -- ------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
Q1 Q2 Q3 Q= 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
-- -- -- ------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
all.Phred(B) 18 40 40 0.2 0.9 0.5 1.0 1.5 1.9 1.1 1.2 1.3 1.4 3.0 1.5 1.6 1.6 1.6 1.5 1.5 1.5 1.5 1.4 1.4 1.4 1.3 1.3 1.2 1.2 1.2 1.1 1.1 1.1 1.0 1.0 1.0 1.0 0.9 0.9 0.9 0.9 0.8 0.8 51.0
avg.Phred(R) 26 30 34 0.1 0.0 0.0 0.0 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.3 0.3 0.3 0.4 0.4 0.5 0.6 0.8 1.0 1.3 1.6 2.1 2.7 3.5 4.2 5.1 5.8 6.5 7.0 7.3 7.3 7.1 6.7 6.2 5.5 4.8 3.9 3.0 1.9 0.7
no.Errors(E) 0 1 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FQreport is expected to run four times faster than FastQC on uncompressed FASTQ files. However, to obtain faster running times, the stream editor sed can be used to read every b th FASTQ block. Using small value of b (e.g. b ≤ 10) generally does not significantly affect the overall results in the outputted table, e.g.
b=3; x=$(( $b * 4 ));
gunzip SRR001666_2.fastq.gz ;
sed -n "1~$x p;2~$x p;3~$x p;4~$x p" SRR001666_2.fastq | fqreport -f SRR001666_2 However, in such a case, be aware that the two first values no.reads(NR) and no.bases(NB) will therefore be reduced:
##File: SRR001666_2
#no.reads(NR): 2349223
#no.bases(NB): 84572028
#avg.lgt(AL): 36.0
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
n Lfreq pA pC pG pT pN Efreq Q1 Q2 Q3 Q= 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
----- ------ ------ ------ ------ ------ ------ ------ -- -- -- ------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
0 . . . . . . 47.11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1 . 27.40 24.17 23.30 25.03 0.09 26.30 40 40 40 0.1 0.0 0.0 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 94.2
2 . 27.20 23.35 23.79 25.53 0.13 12.44 40 40 40 0.1 0.0 0.0 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 94.2
3 . 25.56 24.86 24.24 25.16 0.18 5.92 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 92.3
4 . 24.57 25.20 25.18 24.83 0.22 3.01 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 92.3
5 . 24.88 24.23 25.62 25.06 0.21 1.67 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.3 0.1 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 91.5
6 . 24.64 25.46 25.43 24.22 0.25 0.98 40 40 40 0.2 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.3 0.1 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 90.6
7 . 24.82 24.53 25.74 24.70 0.21 0.64 40 40 40 0.2 0.1 0.0 0.1 0.2 0.2 0.1 0.1 0.1 0.2 0.4 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 87.4
8 . 24.94 25.00 25.04 24.81 0.21 0.44 40 40 40 0.2 0.1 0.0 0.1 0.2 0.2 0.1 0.1 0.1 0.2 0.4 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 86.8
9 . 24.43 25.30 25.26 24.78 0.23 0.32 40 40 40 0.2 0.1 0.1 0.1 0.2 0.3 0.2 0.2 0.2 0.2 0.5 0.3 0.3 0.3 0.3 0.4 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.7 82.7
10 . 24.81 25.12 25.51 24.32 0.25 0.24 40 40 40 0.2 0.1 0.1 0.1 0.2 0.3 0.2 0.2 0.2 0.2 0.6 0.3 0.3 0.4 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.8 0.8 80.6
11 . 24.64 25.29 25.28 24.53 0.26 0.19 40 40 40 0.3 0.1 0.1 0.2 0.3 0.3 0.2 0.2 0.2 0.3 0.6 0.3 0.4 0.4 0.4 0.5 0.5 0.5 0.5 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.7 0.7 0.7 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 0.8 78.6
12 . 24.46 25.53 25.41 24.39 0.21 0.14 39 40 40 0.2 0.1 0.1 0.2 0.3 0.4 0.2 0.3 0.3 0.3 0.8 0.4 0.5 0.5 0.5 0.6 0.6 0.6 0.7 0.7 0.7 0.7 0.8 0.8 0.8 0.8 0.8 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 0.9 1.0 1.0 1.0 74.4
13 . 24.68 25.29 25.40 24.38 0.25 0.11 35 40 40 0.3 0.2 0.1 0.2 0.3 0.4 0.3 0.3 0.3 0.4 0.8 0.5 0.5 0.6 0.6 0.7 0.7 0.7 0.8 0.8 0.9 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.0 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 70.0
14 . 24.64 25.32 25.28 24.51 0.26 0.09 33 40 40 0.3 0.2 0.1 0.2 0.4 0.5 0.3 0.3 0.4 0.4 0.9 0.5 0.6 0.6 0.7 0.7 0.8 0.8 0.9 0.9 0.9 1.0 1.0 1.0 1.0 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.2 1.2 1.2 1.1 1.1 1.1 1.1 67.8
15 . 24.37 25.63 25.34 24.42 0.24 0.07 31 40 40 0.2 0.2 0.1 0.2 0.4 0.5 0.3 0.4 0.4 0.5 1.1 0.6 0.7 0.7 0.8 0.8 0.9 0.9 1.0 1.0 1.0 1.0 1.1 1.1 1.1 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 1.2 64.9
16 . 24.49 25.48 25.49 24.30 0.24 0.05 28 40 40 0.2 0.3 0.1 0.3 0.5 0.7 0.4 0.4 0.5 0.6 1.3 0.8 0.8 0.9 0.9 1.0 1.0 1.1 1.1 1.2 1.2 1.2 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 1.3 59.8
17 . 24.38 25.61 25.38 24.41 0.21 0.03 25 40 40 0.2 0.3 0.2 0.3 0.6 0.8 0.5 0.5 0.6 0.7 1.6 0.9 1.0 1.1 1.1 1.2 1.2 1.3 1.3 1.4 1.4 1.4 1.4 1.4 1.4 1.5 1.5 1.5 1.5 1.4 1.5 1.4 1.4 1.4 1.4 1.4 1.4 1.3 1.3 1.3 54.9
18 . 24.16 25.74 25.43 24.26 0.40 0.02 24 40 40 0.4 0.3 0.2 0.4 0.6 0.8 0.5 0.6 0.7 0.7 1.8 1.0 1.1 1.2 1.2 1.3 1.3 1.4 1.4 1.5 1.5 1.5 1.5 1.6 1.6 1.6 1.6 1.6 1.5 1.5 1.5 1.5 1.5 1.5 1.4 1.4 1.4 1.4 1.3 1.3 52.2
19 . 24.38 25.67 25.53 24.18 0.24 0.01 22 39 40 0.2 0.3 0.2 0.4 0.7 1.0 0.6 0.7 0.8 0.9 2.0 1.1 1.2 1.3 1.4 1.4 1.5 1.5 1.6 1.6 1.6 1.6 1.7 1.7 1.7 1.7 1.7 1.6 1.6 1.6 1.6 1.5 1.5 1.5 1.5 1.4 1.4 1.4 1.3 1.3 48.8
20 . 24.29 25.66 25.45 24.35 0.25 0.01 20 35 40 0.3 0.4 0.2 0.5 0.9 1.2 0.7 0.8 0.9 1.0 2.4 1.4 1.4 1.5 1.6 1.6 1.7 1.7 1.7 1.8 1.8 1.8 1.8 1.8 1.8 1.8 1.8 1.7 1.7 1.7 1.6 1.6 1.6 1.5 1.5 1.4 1.4 1.4 1.3 1.3 43.9
21 . 24.07 25.89 25.49 24.25 0.29 0.01 19 33 40 0.3 0.5 0.3 0.6 1.0 1.3 0.8 0.9 1.0 1.2 2.7 1.5 1.6 1.7 1.7 1.8 1.8 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.9 1.8 1.8 1.8 1.8 1.7 1.7 1.6 1.6 1.5 1.5 1.4 1.4 1.4 1.3 1.3 40.7
22 . 24.26 25.73 25.55 24.20 0.25 0.01 18 31 40 0.3 0.5 0.3 0.7 1.1 1.4 0.9 1.0 1.2 1.3 3.0 1.7 1.8 1.8 1.9 2.0 2.0 2.0 2.1 2.1 2.1 2.0 2.0 2.0 2.0 1.9 1.9 1.8 1.8 1.7 1.7 1.6 1.6 1.5 1.5 1.4 1.4 1.3 1.3 1.2 37.2
23 . 24.26 25.65 25.45 24.36 0.29 0.01 16 28 40 0.3 0.6 0.4 0.8 1.2 1.7 1.0 1.2 1.3 1.5 3.4 1.9 2.0 2.1 2.1 2.2 2.2 2.2 2.2 2.2 2.2 2.2 2.1 2.1 2.0 2.0 1.9 1.9 1.8 1.7 1.7 1.6 1.6 1.5 1.4 1.4 1.3 1.3 1.2 1.2 33.2
24 . 24.09 25.84 25.54 24.27 0.26 0.01 15 26 40 0.3 0.8 0.4 0.9 1.4 1.9 1.2 1.4 1.6 1.7 3.9 2.2 2.2 2.3 2.4 2.4 2.4 2.4 2.4 2.4 2.3 2.3 2.2 2.2 2.1 2.0 1.9 1.9 1.8 1.7 1.6 1.6 1.5 1.4 1.4 1.3 1.3 1.2 1.1 1.1 29.4
25 . 24.20 25.86 25.59 24.14 0.21 0.01 13 24 40 0.2 0.9 0.5 1.1 1.7 2.3 1.4 1.6 1.8 2.0 4.4 2.4 2.5 2.6 2.6 2.6 2.6 2.6 2.5 2.5 2.4 2.3 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.7 1.6 1.5 1.4 1.4 1.3 1.2 1.2 1.1 1.1 1.0 26.0
26 . 24.10 25.89 25.46 24.34 0.20 0.01 12 22 38 0.2 1.0 0.6 1.2 2.0 2.6 1.6 1.8 2.0 2.2 4.8 2.6 2.7 2.7 2.7 2.7 2.7 2.7 2.6 2.5 2.4 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 1.5 1.4 1.3 1.2 1.2 1.1 1.1 1.0 1.0 23.4
27 . 23.90 26.07 25.59 24.25 0.20 0.01 12 21 36 0.2 1.2 0.7 1.4 2.2 2.9 1.8 2.0 2.2 2.4 5.2 2.8 2.8 2.9 2.9 2.8 2.8 2.7 2.7 2.6 2.5 2.3 2.3 2.1 2.0 1.9 1.8 1.8 1.7 1.6 1.5 1.4 1.3 1.3 1.2 1.1 1.1 1.0 1.0 0.9 21.3
28 . 24.00 25.98 25.61 24.19 0.22 0.01 11 19 33 0.2 1.4 0.8 1.6 2.5 3.3 2.0 2.2 2.4 2.6 5.7 3.0 3.0 3.0 3.0 2.9 2.9 2.8 2.7 2.6 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.3 1.2 1.1 1.0 1.0 0.9 0.9 0.8 19.0
29 . 23.93 25.74 25.52 24.37 0.44 0.01 10 18 31 0.4 1.6 0.9 1.8 2.8 3.6 2.2 2.4 2.6 2.8 6.0 3.1 3.1 3.1 3.1 3.0 2.9 2.8 2.7 2.6 2.4 2.3 2.2 2.0 1.9 1.8 1.7 1.6 1.5 1.4 1.3 1.3 1.2 1.1 1.1 1.0 0.9 0.9 0.8 0.8 17.3
30 . 23.68 26.18 25.55 24.31 0.28 0.01 10 17 29 0.3 1.8 1.1 2.1 3.2 4.1 2.4 2.7 2.9 3.1 6.4 3.3 3.3 3.2 3.1 3.0 2.9 2.8 2.7 2.5 2.4 2.2 2.1 2.0 1.8 1.7 1.6 1.5 1.4 1.3 1.2 1.2 1.1 1.0 1.0 0.9 0.9 0.8 0.8 0.7 15.4
31 . 23.71 25.91 25.53 24.61 0.25 0.01 9 16 28 0.2 2.1 1.3 2.3 3.5 4.6 2.7 2.9 3.1 3.3 6.8 3.4 3.4 3.3 3.2 3.0 2.9 2.8 2.6 2.5 2.3 2.2 2.0 1.9 1.8 1.7 1.5 1.4 1.3 1.2 1.2 1.1 1.0 1.0 0.9 0.8 0.8 0.7 0.7 0.7 13.8
32 . 23.67 25.83 25.40 24.84 0.26 0.01 9 15 26 0.3 2.5 1.5 2.6 3.9 5.0 2.9 3.1 3.3 3.5 7.1 3.5 3.4 3.3 3.2 3.1 2.9 2.7 2.6 2.4 2.2 2.1 1.9 1.8 1.7 1.6 1.4 1.3 1.2 1.2 1.1 1.0 1.0 0.9 0.8 0.8 0.7 0.7 0.6 0.6 12.6
33 . 23.41 26.10 25.51 24.77 0.21 0.01 8 14 24 0.2 2.9 1.7 3.0 4.4 5.5 3.1 3.4 3.5 3.6 7.4 3.6 3.5 3.4 3.2 3.0 2.9 2.7 2.5 2.3 2.2 2.0 1.8 1.7 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.9 0.8 0.8 0.7 0.7 0.6 0.6 0.5 11.0
34 . 23.39 26.12 25.51 24.77 0.21 0.02 7 13 23 0.2 3.3 1.9 3.3 4.8 6.0 3.4 3.6 3.8 3.8 7.6 3.7 3.6 3.4 3.2 3.0 2.8 2.6 2.4 2.2 2.0 1.9 1.8 1.6 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.9 0.8 0.7 0.7 0.6 0.6 0.6 0.5 0.5 9.8
35 . 23.24 25.90 25.60 25.00 0.26 0.04 6 12 22 0.3 3.9 2.2 3.7 5.2 6.4 3.6 3.8 3.9 3.9 7.8 3.8 3.6 3.4 3.1 2.9 2.7 2.5 2.3 2.1 2.0 1.8 1.7 1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.9 0.8 0.7 0.7 0.6 0.6 0.6 0.5 0.5 0.5 8.8
36 100.00 22.91 25.89 25.71 25.27 0.22 0.06 6 12 21 0.2 4.1 2.3 4.0 5.6 6.6 3.7 3.8 3.9 3.9 7.7 3.6 3.4 3.3 3.0 2.8 2.6 2.4 2.2 2.1 1.9 1.7 1.6 1.5 1.3 1.2 1.2 1.1 1.0 0.9 0.8 0.8 0.7 0.7 0.6 0.6 0.5 0.5 0.5 0.4 9.0
----- ------ ------ ------ ------ ------ ------ ------ -- -- -- ------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
Q1 Q2 Q3 Q= 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
-- -- -- ------ ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- -----
all.Phred(B) 18 40 40 0.2 0.9 0.5 1.0 1.5 1.9 1.1 1.2 1.3 1.4 3.0 1.5 1.6 1.6 1.6 1.5 1.5 1.5 1.5 1.4 1.4 1.4 1.3 1.3 1.2 1.2 1.2 1.1 1.1 1.1 1.0 1.0 1.0 1.0 0.9 0.9 0.9 0.9 0.8 0.8 51.0
avg.Phred(R) 26 30 34 0.1 0.0 0.0 0.0 0.1 0.1 0.1 0.1 0.2 0.2 0.2 0.3 0.3 0.3 0.4 0.4 0.5 0.6 0.8 1.0 1.3 1.7 2.2 2.7 3.5 4.2 5.1 5.8 6.5 7.0 7.3 7.3 7.1 6.7 6.2 5.5 4.8 3.9 3.0 1.9 0.7
no.Errors(E) 0 1 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Edgar RC, Flyvbjerg H (2015) Error filtering, pair assembly and error correction for next-generation sequencing reads. Bioinformatics, 31(21):3476-3482. doi:10.1093/bioinformatics/btv401.
Ewing D, Green P (1998) Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Research, 8:186-194. doi:10.1101/gr.8.3.186.