Quality scores in the Illumina platform

The quality scores in the FASTQ format come in different versions. You can read more about the FASTQ format at http://en.wikipedia.org/wiki/FASTQ_format. When you select to import Illumina data and click Next there is an option to use different quality score schemes at the bottom of the dialog (see figure 6.6).

Image importselectillumunaqualityscores
Figure 6.6: Selecting the quality score scheme.

There are three options:

Small sample of all three kinds of files are shown below. The names of the reads have no influence on the quality score format:

NCBI/Sanger Phred scores:

@SRR001926.1 FC00002:7:1:111:750 length=36
TTTTTGTAAGGAGGGGGGTCATCAAAATTTGCAAAA
+SRR001926.1 FC00002:7:1:111:750 length=36
IIIIIIIIIIIIIIIIIIIIIIIIIFIIII'IB<IH
@SRR001926.7 FC00002:7:1:110:453 length=36
TTATATGGAGGCTTTAAGAGTCATAGGTTGTTCCCC
+SRR001926.7 FC00002:7:1:110:453 length=36
IIIIIIIIIII:'III?=IIIIII+&III/3I8F/&

Illumina Pipeline 1.2 and earlier (note the question mark at the end of line 4 - this is one of the values that are unique to the old Illumina pipeline format):

@SLXA-EAS1_89:1:1:672:654/1
GCTACGGAATAAAACCAGGAACAACAGACCCAGCA
+SLXA-EAS1_89:1:1:672:654/1
cccccccccccccccccccc]c``cVcZccbSYb?
@SLXA-EAS1_89:1:1:657:649/1
GCAGAAAATGGGAGTGAAAATCTCCGATGAGCAGC
+SLXA-EAS1_89:1:1:657:649/1
ccccccccccbccbccb``cccbcccZcc`^bR^`
The formulas used for converting the special Solexa-scale quality scores to Phred-scale:

$ Q_{phred} = -10 \log_{10} p$

$ Q_{solexa} = -10 \log_{10} \frac{p}{1-p}$

A sample of the quality scores of the Illumina Pipeline 1.3 and 1.4:

@HWI-E4_9_30WAF:1:1:8:178
GCCAGCGGCGCAAAATGNCGGCGGCGATGACCTTC
+HWI-E4_9_30WAF:1:1:8:178
babaaaa\ababaaaaREXabaaaaaaaaaaaaaa
@HWI-E4_9_30WAF:1:1:8:1689
GATGGAGATCTCGACCTNATAGGTGCCCTCATCGG
+HWI-E4_9_30WAF:1:1:8:1689
aab`]_aaaaaaaaaa[ER`abaaa\aaaaaaaa[
Note that it is not possible to see from that data itself that it is actually not Illumina Pipeline 1.2 and earlier, since they use the same range of ASCII values.

To learn more about ASCII values, please see http://en.wikipedia.org/wiki/Ascii#ASCII_printable_characters.