IGV (Integrative Genomics Viewer) is a high-performance genomic data visualization tool that can help users to synthesize and analyze different types of genomic data at the same time, and can flexibly amplify a specific area of the genome. IGV software can be downloaded for free from: http://www.broadinstitute.org/igv. IGV can view SAM/BAM comparison files and VCF mutation detection files. The figure below shows the IGV visualization window.

All data is compressed into *.tar.gz file format with "tar -czvf" under linux system, please decompress according to the following method:

Unix/Linux user: tar -zxvf *.tar.gz

Windows usr: suggest winRAR software

Mac user: shell command: tar -zxvf *.tar.gz, suggest: 'stuffit expander'

The following list shows the structure of delivery data file list, you can focus on the structure for the directories which are included in the directory.

The base quality of Cyclone  FASTQ 

FASTQ

The file storing the sequence and the corresponding quality value, the sequence and the quality value are expressed in  ASCII 

ASCII

ASCII, the American Standard Information Interchange Code, is a computer coding system based on the Latin alphabet and used to display modern English and other Western European languages.

code

data is calculated using Phred. The Phred value is calculated during the base calling process using a model that predicts the probability of base errors. If the sequencing error rate is represented by E and the base quality value is represented by SQ, the following relationship exists:

SQ = -10log10E

The concise correspondence between the quality value and Phred score of the base is shown in the following table: