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= Introduction =
= Introduction =
The qplot program calculates various summary statistics some of which will be plotted in a PDF file that 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 are calculated based on the background mismatch rate. Background mismatch rate is 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.
The qplot program calculates various summary statistics some of which are plotted in a PDF file. These statistics can be used to assess the sequencing quality of Illumina sequence reads mapped to the reference genome. The main statistics are empirical Phred scores which are calculated based on the background mismatch rate. Background mismatch rate is 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 you through: [[#Where to Find It |how to obtain qplot]], [[#Usage |how to use qplot]], [[#Built-in example |example outputs]], [[#anchorOfInteractiveQplot |interactive diagnostic plots]], and [[#Diagnose sequencing quality |real applications]] in which qplot has helped identify sequencing problems.
In the following sections, we will guide you through: [[#Where to Find It |how to obtain qplot]], [[#Usage |how to use qplot]], [[#Built-in example |example outputs]], [[#anchorOfInteractiveQplot |interactive diagnostic plots]], and [[#Diagnose sequencing quality |real applications]] in which qplot has helped identify sequencing problems.
