Summary Report (*.summary.csv)

IDs of samples reported on in the file.

Names of samples reported on in the file.

Run folders for samples reported on in the file.

Reference genome selected.

When true, the input sample is paired-end.

When false, the input sample is single-end.

The number of 5' bases cropped from each read during the FASTQ trimming stage.

All 5' bases with a quality score less than this value are removed during the FASTQ trimming stage.

All 3' bases with a quality score less than this value are removed during the FASTQ trimming stage.

When true, the methylation preparation library only contains reads from bisulfite-treated top and bottom strands.

When false, the library contains additional reads complementary to bisulfite-treated top and bottom strand.

When true, PCR duplicates are flagged in the final .bam files. If the input data are single-end, this setting is ignored and no duplicates are marked.

Applies to paired-end reads with an overlap for Read 1 and Read 2. When true, this option tells the app to score methylation calls in the overlap area only one time, which removes a bias towards more methylation calls towards the center of sequenced fragments. This option does not apply to single-end data.

Number of 5' bases to ignore during the methylation calling stage.

When true, a Cytosine Report containing methylation status for every cytosine in the genome (including both strands) is generated, with the file name SampleName_SampleNumber.CX_report.txt.gz. See Cytosine Report (*.CX_report.txt.gz).

Measuring diversity of input library. It is the number of unique input DNA fragments. Because of the low complexity associated with MethylSeq data, this value might not apply.

The number of reads (2x the number of pairs for paired-end data) in the trimmed FASTQ files.

The total number in Read 1 that are aligned to the reference genome.

The total number in Read 2 that are aligned to the reference genome.

The percentage of Read 1 that are aligned to the reference genome.

The percentage of Read 2 that are aligned to the reference genome.

Percentage of paired reads that have duplicates.

Median length of the sequenced fragment. The fragment length is calculated based on the locations at which a read pair aligns to the reference. The read mapping information is parsed from the BAM files.

Minimum length of the sequenced fragment.

Maximum length of the sequenced fragment.

Standard deviation of the sequenced fragment length.

The number of bases passing filter for the sample.

The number of bases passing filter for Read 1.

The number of bases passing filter for Read 2.

Percentage of bases from Read 1 with a quality score of 30 or higher.

Percentage of bases from Read 2 with a quality score of 30 or higher.

The total number of bases present in the data set that aligned to the reference genome.

The total number of bases that are aligned to the reference genome for Read 1.

The total number of bases that are aligned to the reference genome for Read 2.

The percentage of aligned bases for the reads.

The percentage of aligned bases for Read 1.

The percentage of aligned bases for Read 2.

The total number of aligned bases divided by the genome size.

The number of read pairs (or reads when single-end) aligned to the bisulfite-converted top strand of reference genome.

The number of aligned reads that are complementary to the original bisulfite-treated top strand. When the library prep kit is directional, the value is 0.

The number of aligned reads that are the original bisulfite-treated bottom strand.

The number of aligned reads that are complementary to the original bisulfite-treated bottom strand. When the library prep kit is directional, the value is 0.

The number of C bases in aligned reads.

The number of methylated C bases in aligned reads that are in the context of CpG.

The number of methylated C bases in aligned reads that are in the context of CHG.

The number of methylated C bases in aligned reads that are in the context of CHH.

The number of methylated C bases in aligned reads that are in other contexts.

The number of unmethylated C bases in aligned reads that are in the context of CpG.

The number of unmethylated C bases in aligned reads that are in the context of CHG.

The number of unmethylated C bases in aligned reads that are in the context of CHH.

The number of unmethylated C bases in aligned reads that are in other contexts.

The percent of methylated C bases in aligned reads that are in the context of CpG.

The percent of methylated C bases in aligned reads that are in the context of CHG.

The percent of methylated C bases in aligned reads that are in the context of CHH.