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Coverage statistics summary
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A summary of the statistics presented in the tables at the top of the plugin report. The first line is the title. Each subsequent line is either blank or a particular statistic title followed by a colon (:) and its value.
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Base depth of coverage
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Coverage summary data used to create the Depth of Coverage Chart. This file contains the following fields:
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read_depth: the depth at which a (targeted) reference base has been read.
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base_cov: the number of times any base was read (covered) at this depth.
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base_cum_cov: the cumulative number of reads (coverage) at this read depth or greater.
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norm_read_depth: the normalized read depth (depth divided by average base read depth).
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pc_base_cum_cov: same as base_cum_cov but represented as a percentage of the total base reads.
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Amplicon coverage summary
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Coverage summary data used to create the Amplicon Coverage Chart. This file contains these fields:
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contig_id: the name of the chromosome or contig of the reference for this amplicon.
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contig_srt: the start location of the amplicon target region.
This coordinate is 1-based, unlike the corresponding 0-based coordinate in the original targets BED file.
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contig_end: the last base coordinate of this amplicon target region.
Note: The length of the amplicon target is given as tlen = (contig_end - contig_srt + 1).
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region_id: the ID for this amplicon as given as the 4th column of the targets BED file.
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gene_id: the gene symbol as given as the last field of the targets BED file.
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gc_count: the number of G and C bases in the target region. %GC = 100% * gc / tlen.
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overlaps: the number of times this target was overlapped by any read by at least one base.
Individual reads might overlap multiple amplicons where the amplicon regions themselves overlap.
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fwd_e2e: the number of assigned forward strand reads that read from one end of the amplicon region to the other end.
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rev_e2e: the number of assigned reverse strand reads that read from one end of the amplicon region to the other end.
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total_reads: the total number of reads assigned to this amplicon. This value is the sum of fwd_reads and rev_reads and is the field that rows of this file are ordered by (then by contig id, srt and end).
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fwd_reads: the number of forward strand reads assigned to this amplicon.
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rev_reads: the number of reverse strand reads assigned to this amplicon.
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cov20x: the number of bases of the amplicon target that had at least 20 reads.
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cov100x: the number of bases of the amplicon target that had at least 100 reads.
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cov500x: the number of bases of the amplicon target that had at least 500 reads.
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Chromosome base coverage summary
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Base reads per chromosome summary data used to create the default view of the Reference Coverage Chart. This file contains these fields:
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chrom: the name of the chromosome or contig of the reference.
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start: the coordinate of the first base in this chromosome. This is always 1.
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end: the coordinate of the last base of this chromosome. Also its length in bases.
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fwd_reads: the total number of forward strand base reads for the chromosome.
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rev_reads: the total number reverse strand base reads for the chromosome.
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fwd_ontrg (if present): the total number of forward strand base reads that were in at least one target region.
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seq_reads: the total sequencing (whole) reads that are mapped to individual contigs.
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Aligned reads BAM file
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Contains all aligned reads that are used to generate this report, in BAM format. This is the same file that can be downloaded from the main report (for the specific barcode). See the current SAM tools documentation for more file format information.
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Aligned reads BAI file
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Binary BAM index file as required by some analysis tools and alignment viewers such as IGV. This is the same file that can be downloaded from the main report (for the specific barcode).
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