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.

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

QC for reads2 (similar to QC for reads1)

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

Total: number of total reads
Mapped: number of reads mapped on the chromosome
Unique: number of reads with unique mapping position on the chromosomes
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.

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

Please click the title “Methylation sites distribution statistics” to view more information in detail.

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

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

For each chromosome, the reads coverage and the methylated cytosine density 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 across the whole genome for both strands.
The second table shows the mCG/CG, mCHG/CHG, mCHH/CHH in the whole genome.

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

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.

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

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.

This figure shows the number of the high-methylation level CGIs in different functional regions of genes including 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”.

Functional cluster analysis of genes of high- and low-methylation in promoters

Functional cluster analysis of genes of high- or low-methylated gene bodies. 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.

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.

These two figures show the relationship between the gene expression level and methylation level in the CH context.

These two figures show the relationship between the gene expression level and methylation level in the C context.