Viewing Coverage of Target Regions

For exome capture projects, the Coverage of Target Regions report provides information about capture regions for each sample.

To view the report, choose Project > Show coverage of target regions. If prompted, select an exome coverage (.bed) file from the Capture Region file dialog. The .bed file defines capture regions and is generated by the sequence provider. It is normally located together with (or near) your other sequencing files. Once you have selected the file, click Open to launch the report.

The report consists of three tabs.

• Targeted – columns display such information as the amount of coverage for each region by depth and percent, the exome length, and the number of reads and variants in the exome.

Check the Show RPKM Distribution box to view a bar graph showing the distribution of RPKM (reads assigned per kilobase of target per million mapped reads) along the contig.

As with other SeqMan Pro tables, you may sort table by clicking on any column header. When you sort the Coverage of Target Regions table by clicking on a column header, the resulting groups are also shown in different colors (giving a “rainbow” effect) to help visually differentiate between them.

• Not Targeted – similar to the Targeted tab but displays information for non-target regions. This tab does not contain an option for viewing RPKM distribution.

To sort the table information, click on any column header.

• Enrichment Report – contains two unsortable columns with a series of summary statistics pertaining to the quality of the region capture and assembly processes.

The following table describes each row of the Enrichment Report:

Name	Description
Total length of targeted reference	The sum, in base pairs, of the targeted regions specified in the .bed or manifest file, minus any overlapping regions.
Total aligned reads	The sum of the reads in the final alignment from both the targeted and non-targeted regions.
Targeted aligned reads	The sum of the reads in the final alignment from the targeted regions.
Read enrichment	The number of targeted reads divided by the total number of aligned reads, expressed as a percentage.
Total aligned bases	The sum of the bases in the final alignment from all reads in both the targeted and non-targeted regions.
Targeted aligned bases	The sum of the bases in the final alignment from all reads in the targeted regions.
Base enrichment	The number of targeted aligned bases divided by the total aligned bases expressed as a percentage.
Mean region coverage depth	The mean value from the distribution of average coverage depths from all targeted regions.
*Uniformity of coverage (Pct > 0.2mean)**	The percentage of targeted regions with average coverage greater than 20% of the mean region coverage depth.
Target coverage at 1X	The percentage of bases in all targeted regions with a depth of coverage of one or greater.
Target coverage at 10X	The percentage of bases in all targeted regions with a depth of coverage of ten or greater.
Target coverage at 20X	The percentage of bases in all targeted regions with a depth of coverage of twenty or greater.
Target coverage at 50X	The percentage of bases in all targeted regions with a depth of coverage of fifty or greater.
Insert size median	For paired end or mate pair data where both reads are in the final alignment, the median distance between the 5’-most reference position of the upstream read and the 3’-most reference position of the downstream read.
Insert size min	The minimum insert size among all aligned paired ends or mate pair reads.
Insert size max	The maximum insert size among all aligned paired ends or mate pair reads at the 99^th percentile.
Insert size SD	The standard deviation with respect to the mean insert size, assuming a normal distribution.
Insert size 25th percentile	Twenty-five percent of all inserts are equal to or shorter than the specified insert length.
Insert size 75th percentile	Seventy-five percent of all inserts are equal to or shorter than the specified insert length.
SNPs	The total number of called variants, including insertions and deletions, which meet the hard filtering criteria.
SNPs (Percent found in dbSNP)	Percent of the total number of variant positions which meet the filtering criteria and are also found in dbSNP.
SNP Ts/Tv ratio	The number of nucleotide substitutions that are transitions (purine to purine or pyrimidine to pyrimidine), divided by the number that are transversions (purine to pyrimidine or vice versa).
SNP Het/Hom ratio	The number of variant positions called heterozygous, divided by the number of positions called homozygous.

To save the Coverage of Targeted Regions report as a tab-delimited file (.txt), select File > Save Exome Capture Report.

Note for Windows users: In order to view correctly formatted text reports, we recommend using Wordpad, Notepad++, or Microsoft Excel, and not the default Windows text editor, Notepad.