2 Results description
2.1  Job status

The job status bar demonstrates the status of a job in real time, including the status (waiting, running, finished, error) of each step, and the time it took.

2.2  Quality analysis result

QC for reads1
Sequence Duplication Level

Per base sequence quality

Per sequence quality scores

Per base GC content

Per base sequence content

Per sequence GC content

Click on the red hyperlink detail,following two tables will be shown.

2.3  Mapping Result

Total: number of total reads
Mapped: number of reads mapped on the chromosome
Unique: number of reads with unique mapping position on the chromosome
Used: number of reads after removing duplicated reads (optional) and reads mapping on wrong positions
Please click the red hyperlink "download" to download the result.

2.4  mC identification

We use binomial distribution to identify methylcytosines, and then FDR was used to correct it (p = 0.01).

2.4.1 Methylation sites distribution statistics

Clicking the chromosome icon, user could see the read coverage, mC distribution, chromosome coverage rate etc.

In the first figure:
Vertical axis: Genome position
Horizontal axis: average reads coverage
Step size: 100bp
In the second figure:
Vertical axis: Genome position
Horizontal axis: average methylation level
Step size: 10000bp

For each chromosome, the reads coverage and the methylatted cytosine density in the CG context in a defined interval is calculated. The green bar is for the reverse stand and the red bar is for the forward strand. Click the little bar, detail information will be shown using GBrowse which like the below figure.

The first table shows the coverage percentage in the genome-wide for both strands.
The second table shows the number of mCG, mCHG, mCHH in the genome-wide.

A scatter plot shows the absolute methylcytosine level (mC/L) in the CG context in a defined interval (L=10000bp) in the genome-wide.

2.4.2 CG methylation and non-CG methylation ratio

The percentage of methylated Cytosine in different sequence context is presented: CG, CHG and CHH (H = A, T, or C). Please click the title "CG methylation and non-CG methylation ratio" to view more information in detail.

2.4.3 Methylation level distribution in genome-wide

This figure shows the number of methylated cytosine in each methylation level interval.

2.5  Annotation
2.5.1Methylation level distribution: methylation level distribution in genes, methylation level distribution in repeats

The different functional regions of genes include seven parts: upstream, first exon, first intron, inner exons, inner introns, last exon and downstream. The red line is for CG, the blue line is for CHG and the green line is for CHH.
The different regions of repeats include three parts: upstream, repeat, and downstream. The red line is for CG, the blue line is for CHG and the green line is for CHH.

2.5.2 high-methylation level CGI distribution in genes

This figure shows the number of the high-methylation level CGIs in different functional region of genes including in upstream, gene body, downstream, and intergenic spacer. Please click the title "High-methylation level CGI distribution in genes" to view more information in detail..

Users could download the results via the red hyperlink "Results download"

2.5.3 high- and low- methylation gene GO clustering

promoter

Functional cluster analysis of genes of high- and low-methylated in promoters
Please click the title "High- and low-methylation gene GO clustering" to view more information in detail.

These three pictures show the sequence bias of methylation site. These pictures come from a third-party software weblogo.

2.7  Relationship between methylation level and gene expression

These two figures show the relationship between the gene expression level and methylation level in the CG context. The genes are sorted according to the expression level and then divided into 5 groups averagely. For each group of the genes, the number of mCG and CG are counted and the ratio of them is calculated in each defined interval of upstream district. The ratios are averaged over all genes in the same interval. The 1st group genes have the lowest expression level.