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= Introduction =
= Introduction =
The qplot program is to calculate various summary statistics some of which will be plotted in a pdf file which can be used to assess the sequencing quality for illumina sequencing after mapping reads to the reference genome. The main statistics are empirical Phred scores which was calculated based on the background mismatch rate. By background mismatch rate, it means the rate that sequenced bases are different from the reference genome, EXCLUDING dbSNP positions. Other statistics include GC biases, insert size distribution, depth distribution, genome coverage, empirical Q20 count and so on. An example plot and summary text will follow at the end
The qplot program is to calculate various summary statistics some of which will be plotted in a PDF file which can be used to assess the sequencing quality for Illumina sequencing after mapping reads to the reference genome. The main statistics are empirical Phred scores which was calculated based on the background mismatch rate. By background mismatch rate, it means the rate that sequenced bases are different from the reference genome, EXCLUDING dbSNP positions. Other statistics include GC biases, insert size distribution, depth distribution, genome coverage, empirical Q20 count and so on.
In the following sections, we will guide through: [[#Where to Find It |how to obtain qplot]], [[#Usage |how to use qplot]], [[#Build-in example |example outputs]], [[#anchorOfInteractiveQplot |interactive diagnostic plots]] and [[#Diagnose sequencing quality |real applications]] in which qplot has helped identify sequencing problems.
= Where to Find It =
= Where to Find It =
