changeset 0:e020be4f281b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
author iuc
date Thu, 10 Oct 2019 17:40:46 -0400
parents
children 1672b9bea89b
files qualimap_counts.xml qualimap_macros.xml test-data/coverage_across_reference.txt test-data/coverage_histogram.txt test-data/duplication_rate_histogram.txt test-data/features.gtf test-data/genome_fraction_coverage.txt test-data/genome_results_default.txt test-data/genome_results_inside_features.txt test-data/genome_results_outside_features.txt test-data/mapped_reads_clipping_profile.txt test-data/mapped_reads_gc-content_distribution.txt test-data/mapped_reads_nucleotide_content.txt test-data/mapping_quality_across_reference.txt test-data/mapping_quality_histogram.txt test-data/mouse_counts_ensemble_1000_6.tsv test-data/per_base_coverage_default.txt test-data/per_base_coverage_inside_features.txt test-data/per_base_coverage_outside_features.txt test-data/rnaseq_qc_counts_custom.txt test-data/rnaseq_qc_results_custom.txt test-data/rnaseq_qc_results_default.txt test-data/test_mapped_reads.bam
diffstat 23 files changed, 3617 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_counts.xml	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,442 @@
+<tool id="qualimap_counts" name="QualiMap Counts QC" version="@VERSION@">
+    <macros>
+        <import>qualimap_macros.xml</import>
+        <xml name="gene_info">
+            <conditional name="gene_info">
+                <param name="source" type="select"
+                label="Additional information about genes">
+                    <option value="">None</option>
+                    <option value="builtin">Built-in gene information for supported species</option>
+                    <option value="custom">Custom gene information</option>
+                </param>
+                <when value="" />
+                <when value="builtin">
+                    <param argument="-s" name="species" type="select"
+                    label="Select species">
+                        <option value="HUMAN">Human</option>
+                        <option value="MOUSE">Mouse</option>
+                    </param>
+                </when>
+                <when value="custom">
+                    <param argument="-i" name="info" type="data" format="tsv"
+                    label="Qualimap compatible gene annotation data" />
+                </when>
+            </conditional>
+        </xml>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        @SET_JAVA_OPTS@ &&
+
+        ## Inconveniently, metadata.column_names is a long string of
+        ## comma-separated, sanitized column name representations.
+        ## The following turns this string into a list of the actual names.
+        #set $sample_names = [
+          s.strip().replace(' ', '_')
+          for s in $input.metadata.column_names
+          .replace('__ob__','')
+          .replace('u__sq__','')
+          .replace('__sq__','')
+          .replace('__cb__','')
+          .split(',')
+        ][1:]
+        #if str($analysis.groups).strip():
+          #set $groups = [
+            v.strip().replace(' ', '_')
+            for v in str($analysis.groups).split(',')
+          ]
+        #else:
+          #set $groups = ['.'] * (int($input.metadata.columns) - 1)
+        #end if
+        #for $col, $sample, $group in zip(range(2, int($input.metadata.columns) + 1), $sample_names, $groups):
+          printf '%s\t%s\tcounts_data\t%d\n' '${sample}' '${group}' ${col} >> data_spec.txt &&
+        #end for
+
+        ln -s '$input' counts_data &&
+
+        qualimap counts
+        --data data_spec.txt
+        #if str($analysis.mode) == 'comparison':
+          --compare
+        #end if
+        #if str($analysis.mode) != 'multi_sample':
+          #if str($analysis.gene_info.source) == 'builtin':
+            --species ${analysis.gene_info.species}
+          #elif str($analysis.gene_info.source) == 'custom':
+            --info ${analysis.info}
+          #end if
+        #end if
+        --threshold $threshold
+        -outdir results -outformat html &&
+
+        #if str($analysis.mode) == 'comparison':
+            #set $report_name = 'ComparisonReport'
+        #elif str($analysis.mode) == 'multi_sample':
+            #set $report_name = 'GlobalReport'
+        #else:
+            #set $sample = $sample_names[int($analysis.sample_number) - 1]
+            ## Qualimap replaces '-' in sample names with '_' for
+            ## determining file names
+            #set $report_name = str($sample).replace('-', '_') + 'Report'
+        #end if
+        #set $summary_report = None
+        @MASSAGE_OUTPUT@
+    ]]></command>
+
+    <inputs>
+        <param name="input" type="data" format="tsv" label="Input counts data" />
+        <conditional name="analysis">
+            <param name="mode" type="select" label="Type of analysis to perform">
+                <option value="multi_sample">Report overview stats for all samples</option>
+                <option value="single_sample">Report feature count stats of a single sample</option>
+                <option value="comparison">Compare two groups of samples</option>
+            </param>
+            <when value="multi_sample">
+                <param name="groups" type="hidden" value="" />
+            </when>
+            <when value="single_sample">
+                <param name="groups" type="hidden" value="" />
+                <param name="sample_number" type="integer" value="1" min="1"
+                label="Which sample in the input would you like to analyze?" />
+                <expand macro="gene_info" />
+            </when>
+            <when value="comparison">
+                <param name="groups" type="text"
+                label="Assign each sample to one of two groups"
+                help="The 'Comparison' mode currently works for exactly two groups of samples. Enter comma-separated group names - one for each sample. The group names will be assigned to the samples in the order of the sample columns of the counts data.">
+                    <validator type="expression" message="Please specify a comma-separated list of group names. No group name in the list may be blank.">all(v.strip() for v in value.split(','))</validator>
+                    <validator type="expression" message="Please specify a comma-separated list of group names. Only two different group names are allowed.">len(set(v.strip() for v in value.split(','))) == 2</validator>
+                </param>
+                <expand macro="gene_info" />
+            </when>
+        </conditional>
+        <param argument="-k" name="threshold" type="integer" value="5" min="1"
+        label="Counts threshold" />
+    </inputs>
+    <outputs>
+        <data name="output_html" format="html" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="mouse_counts_ensemble_1000_6.tsv" ftype="tsv" />
+            <conditional name="analysis">
+                <param name="mode" value="single_sample" />
+                <param name="sample_number" value="3" />
+            </conditional>
+            <assert_command>
+                <has_text text="results/_GlcN03Report.html" />
+            </assert_command>
+            <output name="output_html">
+                <assert_contents>
+                    <has_text text="Qualimap Report: Counts QC" />
+                    <not_has_text text="#Counts Distribution" />
+                    <not_has_text text="#Features With Low Counts" />
+                    <not_has_text text="#Bio Detection" />
+                    <not_has_text text="#Counts Per Biotype" />
+                    <not_has_text text="#Length Bias" />
+                    <not_has_text text="#GC Bias" />
+                    <not_has_text text="#Counts Density" />
+                    <not_has_text text="#Scatterplot Matrix" />
+                    <has_text text="#Saturation" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="mouse_counts_ensemble_1000_6.tsv" ftype="tsv" />
+            <conditional name="analysis">
+                <param name="mode" value="single_sample" />
+                <param name="sample_number" value="3" />
+                <conditional name="gene_info">
+                    <param name="source" value="builtin" />
+                    <param name="species" value="MOUSE" />
+                </conditional>
+            </conditional>
+            <assert_command>
+                <has_text text="results/_GlcN03Report.html" />
+            </assert_command>
+            <output name="output_html">
+                <assert_contents>
+                    <has_text text="Qualimap Report: Counts QC" />
+                    <not_has_text text="#Counts Distribution" />
+                    <not_has_text text="#Features With Low Counts" />
+                    <has_text text="#Bio Detection" />
+                    <has_text text="#Counts Per Biotype" />
+                    <has_text text="#Length Bias" />
+                    <has_text text="#GC Bias" />
+                    <not_has_text text="#Counts Density" />
+                    <not_has_text text="#Scatterplot Matrix" />
+                    <has_text text="#Saturation" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="mouse_counts_ensemble_1000_6.tsv" ftype="tsv" />
+            <conditional name="analysis">
+                <param name="mode" value="comparison" />
+                <param name="groups" value="minus,minus,minus,plus,plus,plus" />
+            </conditional>
+            <output name="output_html">
+                <assert_contents>
+                    <has_text text="Qualimap Report: Counts QC" />
+                    <has_text text="#Counts Distribution" />
+                    <has_text text="#Features With Low Counts" />
+                    <not_has_text text="#Bio Detection" />
+                    <not_has_text text="#Counts Per Biotype" />
+                    <not_has_text text="#Length Bias" />
+                    <not_has_text text="#GC Bias" />
+                    <not_has_text text="#Counts Density" />
+                    <not_has_text text="#Scatterplot Matrix" />
+                    <not_has_text text="#Saturation" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="mouse_counts_ensemble_1000_6.tsv" ftype="tsv" />
+            <conditional name="analysis">
+                <param name="mode" value="comparison" />
+                <param name="groups" value="minus,minus,minus,plus,plus,plus" />
+                <conditional name="gene_info">
+                    <param name="source" value="builtin" />
+                    <param name="species" value="MOUSE" />
+                </conditional>
+            </conditional>
+            <output name="output_html">
+                <assert_contents>
+                    <has_text text="Qualimap Report: Counts QC" />
+                    <has_text text="#Counts Distribution" />
+                    <has_text text="#Features With Low Counts" />
+                    <has_text text="#Bio Detection" />
+                    <not_has_text text="#Counts Per Biotype" />
+                    <has_text text="#Length Bias" />
+                    <has_text text="#GC Bias" />
+                    <not_has_text text="#Counts Density" />
+                    <not_has_text text="#Scatterplot Matrix" />
+                    <not_has_text text="#Saturation" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input" value="mouse_counts_ensemble_1000_6.tsv" ftype="tsv" />
+            <conditional name="analysis">
+                <param name="mode" value="multi_sample" />
+            </conditional>
+            <output name="output_html">
+                <assert_contents>
+                    <has_text text="Qualimap Report: Counts QC" />
+                    <has_text text="_GlcN01 ." />
+                    <has_text text="_GlcN02 ." />
+                    <has_text text="_GlcN03 ." />
+                    <has_text text="+GlcN01 ." />
+                    <has_text text="+GlcN02 ." />
+                    <has_text text="+GlcN03 ." />
+                    <has_text text="#input" />
+                    <has_text text="#Counts Density" />
+                    <has_text text="#Scatterplot Matrix" />
+                    <has_text text="#Saturation" />
+                    <has_text text="#Counts Distribution" />
+                    <has_text text="#Features With Low Counts" />
+                    <not_has_text text="#Bio Detection" />
+                    <not_has_text text="#Counts Per Biotype" />
+                    <not_has_text text="#Length Bias" />
+                    <not_has_text text="#GC Bias" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+In RNA-seq experiments, the reads are usually first mapped to a reference genome. It is assumed that if the number of reads mapping to a certain biological feature of interest (gene, transcript, exon, ...) is sufficient, it can be used as an estimation of the abundance of that feature in the sample and interpreted as the quantification of the expression level of the corresponding region.
+
+These count data can be utilized for example to assess differential expression between two or more experimental conditions. Before assessing differential expression analysis, researchers should be aware of some potential limitations of RNA-seq data, as for example:
+
+- Has saturation been reached, or could more features be detected by
+  increasing the sequencing depth?
+
+- Which type of features are being detected in the experiment?
+
+- How good is the quantification of expression in the sample?
+
+All of these questions can be answered by interpreting the plots generated by
+**Qualimap Counts QC**.
+
+
+Input
+=====
+
+The tool accepts tabular input of type `tsv`. It expects gene identifiers in
+the first and the counts for different samples in the following column(s).
+The first line of the input needs to be a header line starting with `#`,
+immediately followed by the name of the gene identifier column, then the sample
+names separated by tabs.
+So, for example::
+
+  #GeneID    Sample1    Sample2
+
+would be a valid header line.
+
+.. class:: infomark
+
+    The *Counts* output of featureCounts represents nearly valid input for the
+    tool, but you will have to **replace** the header line to add a leading `#`
+    and to provide more telling sample names.
+
+    You can **join** the outputs of several featureCounts runs to obtain
+    multi-sample counts data.
+
+
+Analysis/Report types
+---------------------
+
+*Report overview stats for all samples* - Generates overview plots of the
+counts data across all samples.
+
+*Report feature count stats of a single sample* - Generates plots with detailed
+information about a single sample.
+
+*Compare two groups of samples* - Lets you compare groups of samples representing different conditions.
+This version of Qualimap requires all samples to belong to one of two groups.
+
+
+Parameters
+----------
+
+*Additional information about genes* (optional)
+
+Qualimap requires gene annotation data to generate plots (see *Output* section
+below) of
+
+- counts across classes of features
+- feature length and GC content bias in the counts data
+
+, which are available for the single-sample and group comparison reports.
+
+You can provide the annotation data in the form of:
+
+- Built-in gene information for supported species
+
+  For convenience, Qualimap provides the Ensembl annotations for certain species (currently Human and Mouse). In order to use these annotations, Ensembl Gene IDs should be used as the feature IDs on the count files (e.g. ENSG00000251282).
+
+- Custom gene information
+
+  A tabular dataset holding annotations of the features in the counts dataset is
+  required. It must be in a four-column tab-delimited (`tsv`) format, with the
+  feature names or IDs in the first column, the group (*e.g.* the biotype from
+  Ensembl database) in the second column, feature length in the third and feature
+  GC-content in the last column (see this
+  `example <http://kokonech.github.io/qualimap/samples/human.ens68.txt>`__).
+
+  **Make sure to use the same feature IDs in the annotation and in the counts dataset!**
+
+  To generate a Qualimap-compatible info file based on an arbitrary GTF annotation and a genome FASTA file, the developers of Qualimap offer a `Python script for the command line <https://bitbucket.org/kokonech/qualimap/src/master/util/createQualimapInfoFile.py?at=master>`__.
+
+*Counts threshold*
+
+In order to remove the influence of spurious reads, a feature is considered as
+detected if its corresponding number of counts is greater than this threshold.
+
+By default, the threshold value is set to 5 counts, meaning that features having
+less than 5 counts will not be taken into account.
+
+
+Output
+======
+
+Many of the plots that this tool can produce are created using the NOISeq package. The `NOISeq vignette <http://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf>`__ contains a lot of useful information about the plots and how to interpret them. Here we provide a short explanation:
+
+
+Plots of overview stats for all samples
+---------------------------------------
+
+*Counts Density*
+
+This plot shows density of counts computed from the histogram of log-transformed counts. In order to avoid infinite values in case of zero counts the transformation `log2(expr + 0.5)` is applied, where `expr` is the number of read counts for a given feature. Only log-transformed counts having value greater than 1 are plotted.
+
+*Scatterplot Matrix*
+
+The panel shows a scatterplot along with smoothed line (lower panel) and Pearson correlation coefficients (upper panel) for each pair of samples. Plots are generated using log-transformed counts.
+
+*Saturation*
+
+This plot provides information about the level of saturation in the samples, so it helps the user to decide if more sequencing is needed and more features could be detected when increasing the number of reads.
+
+Sequencing depth of each sample (on the x-axis) is plotted against the number of  detected features (on the y-axis). Here, “detected features” refers to features with more than k counts, where k is the *Counts threshold* selected by the user.
+
+The highlighted value is the real sequencing depth of the sample(s). The
+expected results at other sequencing depths are simulated based on random
+sampling of the original data.
+
+*Counts Distribution*
+
+This box plot shows the overall counts distribution of each sample.
+
+*Features With Low Counts*
+
+This plot shows the proportion of features with low counts in each sample. Such features are usually less reliable and could be filtered out. In this plot, the bars show the percentage of features within each sample having more than 0 counts per million (CPM), or more than 1, 2, 5 and 10 CPM.
+
+
+Plots of single-sample count statistics
+---------------------------------------
+
+.. class:: infomark
+
+    Note that most single-sample plots require built-in or custom *additional
+    information about genes* to be generated. The *Saturation* plot is the only
+    exception.
+
+*Saturation*
+
+Similar to the same plot in the overview of all samples.
+The single-sample plot, however, has an additional y-axis (on the right)
+showing the number of features expected to be newly detected when increasing
+the sequencing depth by one million reads from each indicated sequencing depth
+value.
+
+*Bio Detection*
+
+This barplot allows the user to know which **kind** of features are being
+detected in the chosen sample. The x-axis shows all feature categories listed
+in the annotations file. The gray bars are the percentage of features of each group within the reference genome (or transcriptome, etc.). The striped color bars are the percentages of features of each group detected in the sample with regard to the genome. The solid color bars are the percentages that each group represents in the total detected features in the sample.
+
+*Counts Per Biotype*
+
+This boxplot shows the distribution of counts of features from each detected
+feature clas.
+
+*Length Bias*
+
+The plot describes the relationship between the length of the features and
+their expression values.
+
+Feature lengths are divided into bins, and mean expression of features falling into a particular length interval is computed and plotted. A cubic spline regression model is fitted to explain the relation between length and expression. Coefficient of determination (`R^2`) and p-value are shown together with the regression curve.
+
+*GC Bias*
+
+The plot describes the relantionship between the GC-content of the features and the expression values. The data for the plot is generated similar to the
+*Length Bias* plot. The GC content is divided into bins and the mean expression
+of features falling into any given GC interval is computed. The relation between GC-content and expression is investigated using a cubic spline regression model.
+
+
+Plots for comparing two groups of samples
+-----------------------------------------
+
+This mode can generate side-by-side plots of
+
+- *Counts Distribution*,
+- *Features With Low Counts*
+- *Bio Detection*,
+- *Length Bias* and
+- *GC Bias*
+
+for two groups of samples.
+
+.. class:: infomark
+
+    Note that the *Bio Detection*, *Length Bias* and *GC Bias* plots can only be
+    generated when built-in or custom *additional information about genes* is
+    available.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_macros.xml	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,40 @@
+<macros>
+    <token name="@VERSION@">2.2.2c</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">qualimap</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command>qualimap --help | grep 'QualiMap v.' | cut -d '.' -f 2-</version_command>
+    </xml>
+
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btv566</citation>
+            <citation type="doi">10.1093/bioinformatics/bts503</citation>
+            <yield />
+        </citations>
+    </xml>
+
+    <token name="@SET_JAVA_OPTS@">
+        export JAVA_OPTS="-Djava.awt.headless=true -Xmx\${GALAXY_MEMORY_MB:-1024}m"
+    </token>
+
+    <token name="@MASSAGE_OUTPUT@"><![CDATA[
+        sed 's|images_${report_name}/||g;s|css/||g' results/${report_name}.html > '$output_html' &&
+        mkdir '${output_html.extra_files_path}' &&
+        mv results/css/*.css '${output_html.extra_files_path}' &&
+        mv results/css/*.png '${output_html.extra_files_path}' &&
+        if [ -d results/images_${report_name} ]; then
+          mv results/images_${report_name}/* '${output_html.extra_files_path}' &&
+          for file in \$(ls -A results/raw_data_${report_name}); do mv "results/raw_data_${report_name}/\$file" `echo "results/\$file" | sed 's/(//;s/)//'`; done
+        fi
+        #if $summary_report:
+          && mv results/$summary_report results/summary_report.txt
+        #end if
+    ]]></token>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverage_across_reference.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,326 @@
+#Position (bp)	Coverage	Std
+1.5	0.0	0.0
+3.5	0.0	0.0
+5.5	0.0	0.0
+7.5	0.0	0.0
+9.5	0.0	0.0
+11.5	0.0	0.0
+13.5	0.0	0.0
+15.5	0.0	0.0
+17.5	0.0	0.0
+19.5	0.0	0.0
+21.5	0.0	0.0
+23.5	0.0	0.0
+25.5	0.0	0.0
+27.5	0.0	0.0
+29.5	0.0	0.0
+31.5	0.0	0.0
+33.5	0.0	0.0
+35.5	0.0	0.0
+37.5	0.0	0.0
+39.5	0.0	0.0
+41.5	0.0	0.0
+43.5	0.0	0.0
+45.5	0.0	0.0
+47.5	0.0	0.0
+49.5	0.0	0.0
+51.5	0.0	0.0
+53.5	1.0	0.0
+55.5	2.5	1.5811388300841898
+57.5	3.5	1.8708286933869707
+59.5	4.0	0.0
+61.5	5.0	0.0
+63.5	5.0	0.0
+65.5	5.0	0.0
+67.5	5.0	0.0
+69.5	5.0	0.0
+71.5	5.5	2.345207879911715
+73.5	6.0	0.0
+75.5	6.0	0.0
+77.5	7.0	1.0
+79.5	8.0	0.0
+81.5	8.0	0.0
+83.5	9.0	0.0
+85.5	9.5	3.082207001484488
+87.5	10.5	3.24037034920393
+89.5	12.0	0.0
+91.5	13.5	3.6742346141747673
+93.5	15.0	1.0
+95.5	16.5	4.06201920231798
+97.5	17.5	4.183300132670378
+99.5	18.0	0.0
+101.5	21.5	4.636809247747852
+103.5	23.0	0.0
+105.5	23.5	4.847679857416329
+107.5	25.0	0.0
+109.5	25.0	0.0
+111.5	25.0	0.0
+113.5	25.0	0.0
+115.5	26.0	0.0
+117.5	26.0	0.0
+119.5	26.0	0.0
+121.5	26.5	5.1478150704935
+123.5	29.0	0.0
+125.5	32.0	0.0
+127.5	33.0	0.0
+129.5	32.5	5.70087712549569
+131.5	32.5	5.70087712549569
+133.5	32.0	0.0
+135.5	33.5	5.787918451395113
+137.5	33.0	0.0
+139.5	34.0	0.0
+141.5	36.0	1.0
+143.5	37.5	6.123724356957945
+145.5	38.0	0.0
+147.5	38.0	0.0
+149.5	38.0	0.0
+151.5	38.0	0.0
+153.5	36.0	0.0
+155.5	37.0	0.0
+157.5	36.5	6.041522986797286
+159.5	36.5	6.041522986797286
+161.5	36.5	6.041522986797286
+163.5	35.5	5.958187643906492
+165.5	36.5	6.041522986797286
+167.5	36.0	0.0
+169.5	35.0	1.0
+171.5	36.0	0.0
+173.5	35.0	0.0
+175.5	34.5	6.041522986797286
+177.5	32.0	0.0
+179.5	32.0	0.0
+181.5	31.5	5.612486080160912
+183.5	31.5	5.612486080160912
+185.5	32.0	0.0
+187.5	32.0	0.0
+189.5	31.5	5.612486080160912
+191.5	31.0	0.0
+193.5	31.5	5.612486080160912
+195.5	32.0	0.0
+197.5	31.0	1.0
+199.5	28.5	5.338539126015656
+201.5	30.5	5.522680508593631
+203.5	29.5	5.431390245600108
+205.5	31.0	0.0
+207.5	31.5	5.612486080160912
+209.5	31.0	0.0
+211.5	31.0	0.0
+213.5	31.0	0.0
+215.5	30.5	5.522680508593631
+217.5	28.0	0.0
+219.5	27.0	0.0
+221.5	28.0	0.0
+223.5	28.0	0.0
+225.5	29.0	0.0
+227.5	30.0	0.0
+229.5	30.5	5.522680508593631
+231.5	31.5	5.612486080160912
+233.5	33.5	5.787918451395113
+235.5	33.0	0.0
+237.5	32.0	0.0
+239.5	31.0	1.0
+241.5	29.5	5.431390245600108
+243.5	31.5	5.612486080160912
+245.5	29.5	5.431390245600108
+247.5	29.0	0.0
+249.5	28.5	5.338539126015656
+251.5	27.0	0.0
+253.5	27.0	0.0
+255.5	27.0	0.0
+257.5	27.0	0.0
+259.5	27.0	0.0
+261.5	27.0	0.0
+263.5	27.0	0.0
+265.5	27.0	0.0
+267.5	27.0	0.0
+269.5	27.0	0.0
+271.5	27.0	0.0
+273.5	27.0	0.0
+275.5	27.0	0.0
+277.5	27.0	0.0
+279.5	27.0	0.0
+281.5	27.0	0.0
+283.5	27.0	0.0
+285.5	27.0	0.0
+287.5	27.0	0.0
+289.5	27.0	0.0
+291.5	27.0	0.0
+293.5	27.0	0.0
+295.5	27.0	0.0
+297.5	27.0	0.0
+299.5	27.0	0.0
+301.5	0.0	0.0
+303.5	0.0	0.0
+305.5	0.0	0.0
+307.5	0.0	0.0
+309.5	0.0	0.0
+311.5	0.0	0.0
+313.5	0.0	0.0
+315.5	0.0	0.0
+317.5	0.0	0.0
+319.5	0.0	0.0
+321.5	0.0	0.0
+323.5	0.0	0.0
+325.5	0.0	0.0
+327.5	0.0	0.0
+329.5	0.0	0.0
+331.5	0.0	0.0
+333.5	0.0	0.0
+335.5	0.0	0.0
+337.5	0.0	0.0
+339.5	0.0	0.0
+341.5	0.0	0.0
+343.5	0.0	0.0
+345.5	0.0	0.0
+347.5	0.0	0.0
+349.5	0.0	0.0
+351.5	0.0	0.0
+353.5	0.0	0.0
+355.5	0.0	0.0
+357.5	0.0	0.0
+359.5	0.0	0.0
+361.5	0.0	0.0
+363.5	0.0	0.0
+365.5	0.0	0.0
+367.5	0.0	0.0
+369.5	0.0	0.0
+371.5	0.0	0.0
+373.5	0.0	0.0
+375.5	0.0	0.0
+377.5	0.0	0.0
+379.5	0.0	0.0
+381.5	0.0	0.0
+383.5	0.0	0.0
+385.5	0.0	0.0
+387.5	0.0	0.0
+389.5	0.0	0.0
+391.5	0.0	0.0
+393.5	0.0	0.0
+395.5	0.0	0.0
+397.5	0.0	0.0
+399.5	0.0	0.0
+401.5	0.0	0.0
+403.5	0.0	0.0
+405.5	0.0	0.0
+407.5	0.0	0.0
+409.5	0.0	0.0
+411.5	0.0	0.0
+413.5	0.0	0.0
+415.5	0.0	0.0
+417.5	0.0	0.0
+419.5	0.0	0.0
+421.5	0.0	0.0
+423.5	0.0	0.0
+425.5	0.0	0.0
+427.5	0.0	0.0
+429.5	0.0	0.0
+431.5	0.0	0.0
+433.5	0.0	0.0
+435.5	0.0	0.0
+437.5	0.0	0.0
+439.5	0.0	0.0
+441.5	0.0	0.0
+443.5	0.0	0.0
+445.5	0.0	0.0
+447.5	0.0	0.0
+449.5	0.0	0.0
+451.5	0.0	0.0
+453.5	0.0	0.0
+455.5	0.0	0.0
+457.5	0.0	0.0
+459.5	0.0	0.0
+461.5	0.0	0.0
+463.5	0.0	0.0
+465.5	0.0	0.0
+467.5	0.0	0.0
+469.5	0.0	0.0
+471.5	0.0	0.0
+473.5	0.0	0.0
+475.5	0.0	0.0
+477.5	0.0	0.0
+479.5	0.0	0.0
+481.5	0.0	0.0
+483.5	0.0	0.0
+485.5	0.0	0.0
+487.5	0.0	0.0
+489.5	0.0	0.0
+491.5	0.0	0.0
+493.5	0.0	0.0
+495.5	0.0	0.0
+497.5	0.0	0.0
+499.5	0.0	0.0
+501.5	0.0	0.0
+503.5	0.0	0.0
+505.5	0.0	0.0
+507.5	0.0	0.0
+509.5	0.0	0.0
+511.5	0.0	0.0
+513.5	0.0	0.0
+515.5	0.0	0.0
+517.5	0.0	0.0
+519.5	0.0	0.0
+521.5	0.0	0.0
+523.5	0.0	0.0
+525.5	0.0	0.0
+527.5	0.0	0.0
+529.5	0.0	0.0
+531.5	0.0	0.0
+533.5	0.0	0.0
+535.5	0.0	0.0
+537.5	0.0	0.0
+539.5	0.0	0.0
+541.5	0.0	0.0
+543.5	0.0	0.0
+545.5	0.0	0.0
+547.5	0.0	0.0
+549.5	0.0	0.0
+551.5	0.0	0.0
+553.5	0.0	0.0
+555.5	0.0	0.0
+557.5	0.0	0.0
+559.5	0.0	0.0
+561.5	0.0	0.0
+563.5	0.0	0.0
+565.5	0.0	0.0
+567.5	0.0	0.0
+569.5	0.0	0.0
+571.5	0.0	0.0
+573.5	0.0	0.0
+575.5	0.0	0.0
+577.5	0.0	0.0
+579.5	0.0	0.0
+581.5	0.0	0.0
+583.5	0.0	0.0
+585.5	0.0	0.0
+587.5	0.0	0.0
+589.5	0.0	0.0
+591.5	0.0	0.0
+593.5	0.0	0.0
+595.5	0.0	0.0
+597.5	0.0	0.0
+599.5	0.0	0.0
+601.5	0.0	0.0
+603.5	0.0	0.0
+605.5	0.0	0.0
+607.5	0.0	0.0
+609.5	0.0	0.0
+611.5	0.0	0.0
+613.5	0.0	0.0
+615.5	0.0	0.0
+617.5	0.0	0.0
+619.5	0.0	0.0
+621.5	0.0	0.0
+623.5	0.0	0.0
+625.5	0.0	0.0
+627.5	0.0	0.0
+629.5	0.0	0.0
+631.5	0.0	0.0
+633.5	0.0	0.0
+635.5	0.0	0.0
+637.5	0.0	0.0
+639.5	0.0	0.0
+641.5	0.0	0.0
+643.5	0.0	0.0
+645.5	0.0	0.0
+647.5	0.0	0.0
+649.5	0.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/coverage_histogram.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,36 @@
+#Coverage	Number of genomic locations
+0.0	102.0
+1.0	2.0
+2.0	1.0
+3.0	2.0
+4.0	3.0
+5.0	11.0
+6.0	6.0
+8.0	5.0
+9.0	3.0
+10.0	2.0
+11.0	1.0
+12.0	2.0
+13.0	1.0
+14.0	2.0
+16.0	2.0
+17.0	2.0
+18.0	3.0
+21.0	1.0
+22.0	1.0
+23.0	3.0
+24.0	1.0
+25.0	8.0
+26.0	7.0
+27.0	3.0
+28.0	8.0
+29.0	11.0
+30.0	10.0
+31.0	20.0
+32.0	27.0
+33.0	11.0
+34.0	5.0
+35.0	4.0
+36.0	13.0
+37.0	8.0
+38.0	9.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/duplication_rate_histogram.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,51 @@
+#Duplication rate	Coverage
+1.0	57.0
+2.0	8.0
+3.0	3.0
+4.0	0.0
+5.0	0.0
+6.0	0.0
+7.0	0.0
+8.0	0.0
+9.0	0.0
+10.0	0.0
+11.0	0.0
+12.0	0.0
+13.0	0.0
+14.0	0.0
+15.0	0.0
+16.0	0.0
+17.0	0.0
+18.0	0.0
+19.0	0.0
+20.0	0.0
+21.0	0.0
+22.0	0.0
+23.0	0.0
+24.0	0.0
+25.0	0.0
+26.0	0.0
+27.0	0.0
+28.0	0.0
+29.0	0.0
+30.0	0.0
+31.0	0.0
+32.0	0.0
+33.0	0.0
+34.0	0.0
+35.0	0.0
+36.0	0.0
+37.0	0.0
+38.0	0.0
+39.0	0.0
+40.0	0.0
+41.0	0.0
+42.0	0.0
+43.0	0.0
+44.0	0.0
+45.0	0.0
+46.0	0.0
+47.0	0.0
+48.0	0.0
+49.0	0.0
+50.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/features.gtf	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,4 @@
+test_chromosome	test	gene	1	300	.	+	.	gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+test_chromosome	test	transcript	1	300	.	+	.	gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1";
+test_chromosome	test	exon	1	300	.	+	.	gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
+test_chromosome	test	CDS	100	250	.	+	.	gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_fraction_coverage.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,52 @@
+#Coverage (X)	Coverage
+1.0	66.0
+2.0	65.33333333333334
+3.0	65.0
+4.0	64.33333333333334
+5.0	63.333333333333336
+6.0	59.66666666666667
+7.0	57.66666666666667
+8.0	57.66666666666667
+9.0	56.00000000000001
+10.0	55.00000000000001
+11.0	54.33333333333334
+12.0	54.00000000000001
+13.0	53.33333333333334
+14.0	53.00000000000001
+15.0	52.33333333333334
+16.0	52.33333333333334
+17.0	51.66666666666668
+18.0	51.000000000000014
+19.0	50.000000000000014
+20.0	50.000000000000014
+21.0	50.000000000000014
+22.0	49.66666666666668
+23.0	49.33333333333334
+24.0	48.33333333333334
+25.0	48.00000000000001
+26.0	45.33333333333334
+27.0	43.00000000000001
+28.0	42.00000000000001
+29.0	39.33333333333334
+30.0	35.66666666666667
+31.0	32.33333333333334
+32.0	25.66666666666667
+33.0	16.66666666666667
+34.0	13.0
+35.0	11.333333333333329
+36.0	10.0
+37.0	5.666666666666671
+38.0	3.0
+39.0	0.0
+40.0	0.0
+41.0	0.0
+42.0	0.0
+43.0	0.0
+44.0	0.0
+45.0	0.0
+46.0	0.0
+47.0	0.0
+48.0	0.0
+49.0	0.0
+50.0	0.0
+51.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_default.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,122 @@
+BamQC report
+-----------------------------------
+
+>>>>>>> Input
+
+     bam file = /tmp/tmprT4oZK/files/b/1/f/dataset_b1fbaad4-1b5a-4769-8a15-b4cec4de5731.dat
+     outfile = results/genome_results.txt
+
+
+>>>>>>> Reference
+
+     number of bases = 650 bp
+     number of contigs = 1
+
+
+>>>>>>> Globals
+
+     number of windows = 325
+
+     number of reads = 100
+     number of mapped reads = 100 (100%)
+     number of secondary alignments = 1
+
+     number of mapped bases = 12,665 bp
+     number of sequenced bases = 7,465 bp
+     number of aligned bases = 0 bp
+     number of duplicated reads (estimated) = 18
+     duplication rate = 15.85%
+
+
+>>>>>>> Insert size
+
+     mean insert size = 0
+     std insert size = 0
+     median insert size = 0
+
+
+>>>>>>> Mapping quality
+
+     mean mapping quality = 115.8402
+
+
+>>>>>>> ACTG content
+
+     number of A's = 1,910 bp (25.59%)
+     number of C's = 1,902 bp (25.48%)
+     number of T's = 1,497 bp (20.05%)
+     number of G's = 2,156 bp (28.88%)
+     number of N's = 0 bp (0%)
+
+     GC percentage = 54.36%
+
+
+>>>>>>> Mismatches and indels
+
+    general error rate = 0.0118
+    number of mismatches = 149
+
+
+>>>>>>> Coverage
+
+     mean coverageData = 19.4846X
+     std coverageData = 16.5813X
+
+     There is a 45.85% of reference with a coverageData >= 1X
+     There is a 45.38% of reference with a coverageData >= 2X
+     There is a 44.92% of reference with a coverageData >= 3X
+     There is a 44.62% of reference with a coverageData >= 4X
+     There is a 43.85% of reference with a coverageData >= 5X
+     There is a 41.85% of reference with a coverageData >= 6X
+     There is a 40.46% of reference with a coverageData >= 7X
+     There is a 39.85% of reference with a coverageData >= 8X
+     There is a 38.77% of reference with a coverageData >= 9X
+     There is a 38% of reference with a coverageData >= 10X
+     There is a 37.23% of reference with a coverageData >= 11X
+     There is a 36.92% of reference with a coverageData >= 12X
+     There is a 36.46% of reference with a coverageData >= 13X
+     There is a 36.15% of reference with a coverageData >= 14X
+     There is a 35.54% of reference with a coverageData >= 15X
+     There is a 35.23% of reference with a coverageData >= 16X
+     There is a 34.77% of reference with a coverageData >= 17X
+     There is a 34% of reference with a coverageData >= 18X
+     There is a 33.38% of reference with a coverageData >= 19X
+     There is a 33.38% of reference with a coverageData >= 20X
+     There is a 33.23% of reference with a coverageData >= 21X
+     There is a 31.85% of reference with a coverageData >= 22X
+     There is a 31.54% of reference with a coverageData >= 23X
+     There is a 30.92% of reference with a coverageData >= 24X
+     There is a 30.62% of reference with a coverageData >= 25X
+     There is a 28.62% of reference with a coverageData >= 26X
+     There is a 27.54% of reference with a coverageData >= 27X
+     There is a 26.92% of reference with a coverageData >= 28X
+     There is a 25.23% of reference with a coverageData >= 29X
+     There is a 23.38% of reference with a coverageData >= 30X
+     There is a 20.77% of reference with a coverageData >= 31X
+     There is a 16.77% of reference with a coverageData >= 32X
+     There is a 12.15% of reference with a coverageData >= 33X
+     There is a 10.15% of reference with a coverageData >= 34X
+     There is a 8.62% of reference with a coverageData >= 35X
+     There is a 7.38% of reference with a coverageData >= 36X
+     There is a 4% of reference with a coverageData >= 37X
+     There is a 1.85% of reference with a coverageData >= 38X
+     There is a 0.31% of reference with a coverageData >= 39X
+     There is a 0% of reference with a coverageData >= 40X
+     There is a 0% of reference with a coverageData >= 41X
+     There is a 0% of reference with a coverageData >= 42X
+     There is a 0% of reference with a coverageData >= 43X
+     There is a 0% of reference with a coverageData >= 44X
+     There is a 0% of reference with a coverageData >= 45X
+     There is a 0% of reference with a coverageData >= 46X
+     There is a 0% of reference with a coverageData >= 47X
+     There is a 0% of reference with a coverageData >= 48X
+     There is a 0% of reference with a coverageData >= 49X
+     There is a 0% of reference with a coverageData >= 50X
+     There is a 0% of reference with a coverageData >= 51X
+
+
+>>>>>>> Coverage per contig
+
+	test_chromosome	650	12665	19.484615384615385	16.581284452141826
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_inside_features.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,128 @@
+BamQC report
+-----------------------------------
+
+>>>>>>> Input
+
+     bam file = /tmp/tmpB4Sf0A/files/e/d/7/dataset_ed7510d4-c8f3-41fc-8cc1-3b854d9bdf14.dat
+     outfile = results/genome_results.txt
+
+
+>>>>>>> Reference
+
+     number of bases = 650 bp
+     number of contigs = 1
+
+
+>>>>>>> Globals
+
+     number of windows = 325
+
+     number of reads = 100
+     number of mapped reads = 100 (100%)
+     number of secondary alignments = 1
+
+     number of mapped bases = 6,451 bp
+     number of sequenced bases = 5,101 bp
+     number of aligned bases = 0 bp
+     number of duplicated reads (estimated) = 14
+     duplication rate = 16.18%
+
+
+>>>>>>> Globals inside
+
+     regions size = 300 (46.15%)
+     number of mapped reads = 82 (82%)
+
+
+>>>>>>> Insert size
+
+     mean insert size = 0
+     std insert size = 0
+     median insert size = 0
+
+
+>>>>>>> Mapping quality
+
+     mean mapping quality = 251.3687
+
+
+>>>>>>> ACTG content
+
+     number of A's = 1,243 bp (24.37%)
+     number of C's = 1,257 bp (24.64%)
+     number of T's = 985 bp (19.31%)
+     number of G's = 1,616 bp (31.68%)
+     number of N's = 0 bp (0%)
+
+     GC percentage = 56.32%
+
+
+>>>>>>> Mismatches and indels
+
+    general error rate = 0.0211
+    number of mismatches = 136
+
+
+>>>>>>> Coverage
+
+     mean coverageData = 21.5033X
+     std coverageData = 15.658X
+
+     There is a 66% of reference with a coverageData >= 1X
+     There is a 65.33% of reference with a coverageData >= 2X
+     There is a 65% of reference with a coverageData >= 3X
+     There is a 64.33% of reference with a coverageData >= 4X
+     There is a 63.33% of reference with a coverageData >= 5X
+     There is a 59.67% of reference with a coverageData >= 6X
+     There is a 57.67% of reference with a coverageData >= 7X
+     There is a 57.67% of reference with a coverageData >= 8X
+     There is a 56% of reference with a coverageData >= 9X
+     There is a 55% of reference with a coverageData >= 10X
+     There is a 54.33% of reference with a coverageData >= 11X
+     There is a 54% of reference with a coverageData >= 12X
+     There is a 53.33% of reference with a coverageData >= 13X
+     There is a 53% of reference with a coverageData >= 14X
+     There is a 52.33% of reference with a coverageData >= 15X
+     There is a 52.33% of reference with a coverageData >= 16X
+     There is a 51.67% of reference with a coverageData >= 17X
+     There is a 51% of reference with a coverageData >= 18X
+     There is a 50% of reference with a coverageData >= 19X
+     There is a 50% of reference with a coverageData >= 20X
+     There is a 50% of reference with a coverageData >= 21X
+     There is a 49.67% of reference with a coverageData >= 22X
+     There is a 49.33% of reference with a coverageData >= 23X
+     There is a 48.33% of reference with a coverageData >= 24X
+     There is a 48% of reference with a coverageData >= 25X
+     There is a 45.33% of reference with a coverageData >= 26X
+     There is a 43% of reference with a coverageData >= 27X
+     There is a 42% of reference with a coverageData >= 28X
+     There is a 39.33% of reference with a coverageData >= 29X
+     There is a 35.67% of reference with a coverageData >= 30X
+     There is a 32.33% of reference with a coverageData >= 31X
+     There is a 25.67% of reference with a coverageData >= 32X
+     There is a 16.67% of reference with a coverageData >= 33X
+     There is a 13% of reference with a coverageData >= 34X
+     There is a 11.33% of reference with a coverageData >= 35X
+     There is a 10% of reference with a coverageData >= 36X
+     There is a 5.67% of reference with a coverageData >= 37X
+     There is a 3% of reference with a coverageData >= 38X
+     There is a 0% of reference with a coverageData >= 39X
+     There is a 0% of reference with a coverageData >= 40X
+     There is a 0% of reference with a coverageData >= 41X
+     There is a 0% of reference with a coverageData >= 42X
+     There is a 0% of reference with a coverageData >= 43X
+     There is a 0% of reference with a coverageData >= 44X
+     There is a 0% of reference with a coverageData >= 45X
+     There is a 0% of reference with a coverageData >= 46X
+     There is a 0% of reference with a coverageData >= 47X
+     There is a 0% of reference with a coverageData >= 48X
+     There is a 0% of reference with a coverageData >= 49X
+     There is a 0% of reference with a coverageData >= 50X
+     There is a 0% of reference with a coverageData >= 51X
+
+
+>>>>>>> Coverage per contig
+
+	test_chromosome	300	6451	21.503333333333334	15.658011438947867
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_outside_features.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,128 @@
+BamQC report
+-----------------------------------
+
+>>>>>>> Input
+
+     bam file = /tmp/tmprT4oZK/files/6/4/1/dataset_6416c0ca-3ecd-4273-ae01-22f2ac60965d.dat
+     outfile = results/outside_results.txt
+
+
+>>>>>>> Reference
+
+     number of bases = 650 bp
+     number of contigs = 1
+
+
+>>>>>>> Globals
+
+     number of windows = 325
+
+     number of reads = 100
+     number of mapped reads = 100 (100%)
+     number of secondary alignments = 1
+
+     number of mapped bases = 6,214 bp
+     number of sequenced bases = 2,364 bp
+     number of aligned bases = 0 bp
+     number of duplicated reads (estimated) = 4
+     duplication rate = 14.29%
+
+
+>>>>>>> Globals outside
+
+     regions size = 350 (53.85%)
+     number of mapped reads = 18 (18%)
+
+
+>>>>>>> Insert size
+
+     mean insert size = 0
+     std insert size = 0
+     median insert size = 0
+
+
+>>>>>>> Mapping quality
+
+     mean mapping quality = 255
+
+
+>>>>>>> ACTG content
+
+     number of A's = 667 bp (28.21%)
+     number of C's = 645 bp (27.28%)
+     number of T's = 512 bp (21.66%)
+     number of G's = 540 bp (22.84%)
+     number of N's = 0 bp (0%)
+
+     GC percentage = 50.13%
+
+
+>>>>>>> Mismatches and indels
+
+    general error rate = 0.0021
+    number of mismatches = 13
+
+
+>>>>>>> Coverage
+
+     mean coverageData = 17.7543X
+     std coverageData = 16.4764X
+
+     There is a 10.58% of reference with a coverageData >= 1X
+     There is a 10.58% of reference with a coverageData >= 2X
+     There is a 10.58% of reference with a coverageData >= 3X
+     There is a 10.58% of reference with a coverageData >= 4X
+     There is a 10.58% of reference with a coverageData >= 5X
+     There is a 10.58% of reference with a coverageData >= 6X
+     There is a 10.58% of reference with a coverageData >= 7X
+     There is a 10.58% of reference with a coverageData >= 8X
+     There is a 10.58% of reference with a coverageData >= 9X
+     There is a 10.58% of reference with a coverageData >= 10X
+     There is a 10.58% of reference with a coverageData >= 11X
+     There is a 10.58% of reference with a coverageData >= 12X
+     There is a 10.58% of reference with a coverageData >= 13X
+     There is a 10.58% of reference with a coverageData >= 14X
+     There is a 10.58% of reference with a coverageData >= 15X
+     There is a 10.58% of reference with a coverageData >= 16X
+     There is a 10.58% of reference with a coverageData >= 17X
+     There is a 10.58% of reference with a coverageData >= 18X
+     There is a 10.58% of reference with a coverageData >= 19X
+     There is a 10.58% of reference with a coverageData >= 20X
+     There is a 10.58% of reference with a coverageData >= 21X
+     There is a 10.58% of reference with a coverageData >= 22X
+     There is a 10.58% of reference with a coverageData >= 23X
+     There is a 10.58% of reference with a coverageData >= 24X
+     There is a 10.58% of reference with a coverageData >= 25X
+     There is a 10.58% of reference with a coverageData >= 26X
+     There is a 10.58% of reference with a coverageData >= 27X
+     There is a 10.58% of reference with a coverageData >= 28X
+     There is a 10.58% of reference with a coverageData >= 29X
+     There is a 10.58% of reference with a coverageData >= 30X
+     There is a 10.58% of reference with a coverageData >= 31X
+     There is a 10.1% of reference with a coverageData >= 32X
+     There is a 9.62% of reference with a coverageData >= 33X
+     There is a 9.13% of reference with a coverageData >= 34X
+     There is a 7.21% of reference with a coverageData >= 35X
+     There is a 5.29% of reference with a coverageData >= 36X
+     There is a 3.37% of reference with a coverageData >= 37X
+     There is a 1.44% of reference with a coverageData >= 38X
+     There is a 0.96% of reference with a coverageData >= 39X
+     There is a 0% of reference with a coverageData >= 40X
+     There is a 0% of reference with a coverageData >= 41X
+     There is a 0% of reference with a coverageData >= 42X
+     There is a 0% of reference with a coverageData >= 43X
+     There is a 0% of reference with a coverageData >= 44X
+     There is a 0% of reference with a coverageData >= 45X
+     There is a 0% of reference with a coverageData >= 46X
+     There is a 0% of reference with a coverageData >= 47X
+     There is a 0% of reference with a coverageData >= 48X
+     There is a 0% of reference with a coverageData >= 49X
+     There is a 0% of reference with a coverageData >= 50X
+     There is a 0% of reference with a coverageData >= 51X
+
+
+>>>>>>> Coverage per contig
+
+	test_chromosome	4424	6214	1.404611211573237	3.9981701358234454
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapped_reads_clipping_profile.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,76 @@
+#Read position (bp)	Clipping profile
+0.0	16.666666666666664
+1.0	5.555555555555555
+2.0	0.0
+3.0	0.0
+4.0	0.0
+5.0	0.0
+6.0	0.0
+7.0	0.0
+8.0	0.0
+9.0	0.0
+10.0	0.0
+11.0	0.0
+12.0	0.0
+13.0	0.0
+14.0	0.0
+15.0	0.0
+16.0	0.0
+17.0	0.0
+18.0	0.0
+19.0	0.0
+20.0	0.0
+21.0	0.0
+22.0	0.0
+23.0	0.0
+24.0	0.0
+25.0	0.0
+26.0	0.0
+27.0	0.0
+28.0	0.0
+29.0	0.0
+30.0	0.0
+31.0	0.0
+32.0	0.0
+33.0	0.0
+34.0	0.0
+35.0	0.0
+36.0	0.0
+37.0	0.0
+38.0	0.0
+39.0	0.0
+40.0	0.0
+41.0	0.0
+42.0	0.0
+43.0	0.0
+44.0	0.0
+45.0	0.0
+46.0	0.0
+47.0	0.0
+48.0	0.0
+49.0	0.0
+50.0	0.0
+51.0	0.0
+52.0	0.0
+53.0	0.0
+54.0	0.0
+55.0	0.0
+56.0	0.0
+57.0	0.0
+58.0	0.0
+59.0	0.0
+60.0	0.0
+61.0	0.0
+62.0	0.0
+63.0	0.0
+64.0	0.0
+65.0	0.0
+66.0	0.0
+67.0	0.0
+68.0	0.0
+69.0	0.0
+70.0	0.0
+71.0	5.555555555555555
+72.0	11.11111111111111
+73.0	16.666666666666664
+74.0	44.44444444444444
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapped_reads_gc-content_distribution.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,101 @@
+#GC Content (%)	Sample	HUMAN (hg19)
+1.0	0.0	0.0
+2.0	0.0	3.0E-6
+3.0	0.0	3.0E-6
+4.0	0.0	1.0E-5
+5.0	0.0	8.0E-6
+6.0	0.0	1.2000000000000002E-5
+7.0	0.0	6.999999999999999E-6
+8.0	0.0	9.999999999999999E-6
+9.0	0.0	1.6E-5
+10.0	0.0	1.5000000000000002E-5
+11.0	0.0	1.9999999999999998E-5
+12.0	0.0	1.6E-5
+13.0	0.0	1.6E-5
+14.0	0.0	2.4999999999999998E-5
+15.0	0.0	2.2000000000000003E-5
+16.0	0.0	2.6999999999999996E-5
+17.0	0.0	3.3E-5
+18.0	0.0	3.7000000000000005E-5
+19.0	0.0	4.7000000000000004E-5
+20.0	0.0	5.4999999999999995E-5
+21.0	0.0	6.400000000000001E-5
+22.0	0.0	9.3E-5
+23.0	0.0	1.66E-4
+24.0	0.0	3.03E-4
+25.0	0.0	7.059999999999999E-4
+26.0	0.0	0.0016020000000000001
+27.0	0.0	0.0033690000000000005
+28.0	0.0	0.006167999999999999
+29.0	0.0	0.010352
+30.0	0.0	0.015647
+31.0	0.0	0.022148
+32.0	0.0	0.028808
+33.0	0.0	0.035106000000000005
+34.0	0.0	0.041161
+35.0	0.0	0.047408
+36.0	0.0	0.052698999999999996
+37.0	0.0	0.057517000000000006
+38.0	0.0	0.061487999999999994
+39.0	0.0	0.063321
+40.0	0.0	0.060248
+41.0	0.0	0.055508
+42.0	0.0	0.051446000000000006
+43.0	0.0	0.048194
+44.0	0.017857142857142856	0.044423
+45.0	0.0	0.040655000000000004
+46.0	0.03571428571428571	0.03652
+47.0	0.0	0.032315
+48.0	0.017857142857142856	0.028137999999999996
+49.0	0.0	0.02458
+50.0	0.017857142857142856	0.020810000000000002
+51.0	0.0	0.017532
+52.0	0.05357142857142857	0.014506999999999997
+53.0	0.017857142857142856	0.012007
+54.0	0.14285714285714285	0.010018
+55.0	0.08928571428571429	0.008414999999999999
+56.0	0.17857142857142855	0.007258
+57.0	0.03571428571428571	0.006174999999999999
+58.0	0.08928571428571429	0.005363000000000001
+59.0	0.03571428571428571	0.0046159999999999994
+60.0	0.14285714285714285	0.003946
+61.0	0.0	0.0034579999999999993
+62.0	0.03571428571428571	0.002915
+63.0	0.017857142857142856	0.0024610000000000005
+64.0	0.05357142857142857	0.0019950000000000002
+65.0	0.0	0.0016779999999999998
+66.0	0.017857142857142856	0.0013500000000000003
+67.0	0.0	0.001069
+68.0	0.0	8.119999999999999E-4
+69.0	0.0	6.4E-4
+70.0	0.0	5.05E-4
+71.0	0.0	4.0299999999999993E-4
+72.0	0.0	3.2E-4
+73.0	0.0	2.79E-4
+74.0	0.0	2.0700000000000002E-4
+75.0	0.0	2.0099999999999998E-4
+76.0	0.0	1.54E-4
+77.0	0.0	1.12E-4
+78.0	0.0	7.699999999999999E-5
+79.0	0.0	6.3E-5
+80.0	0.0	3.7E-5
+81.0	0.0	2.8000000000000003E-5
+82.0	0.0	1.6E-5
+83.0	0.0	9.0E-6
+84.0	0.0	4.0E-6
+85.0	0.0	0.0
+86.0	0.0	1.0E-6
+87.0	0.0	0.0
+88.0	0.0	0.0
+89.0	0.0	0.0
+90.0	0.0	0.0
+91.0	0.0	0.0
+92.0	0.0	0.0
+93.0	0.0	0.0
+94.0	0.0	0.0
+95.0	0.0	0.0
+96.0	0.0	0.0
+97.0	0.0	0.0
+98.0	0.0	0.0
+99.0	0.0	0.0
+100.0	0.0	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapped_reads_nucleotide_content.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,76 @@
+# Position (bp)	A	C	G	T	N
+0.0	34.177215189873415	21.518987341772153	26.582278481012654	17.72151898734177	0.0
+1.0	23.456790123456788	33.33333333333333	20.98765432098765	22.22222222222222	0.0
+2.0	25.609756097560975	20.73170731707317	35.36585365853659	18.29268292682927	0.0
+3.0	23.170731707317074	28.04878048780488	28.04878048780488	20.73170731707317	0.0
+4.0	31.70731707317073	26.82926829268293	24.390243902439025	17.073170731707318	0.0
+5.0	25.609756097560975	19.51219512195122	34.146341463414636	20.73170731707317	0.0
+6.0	25.609756097560975	23.170731707317074	34.146341463414636	17.073170731707318	0.0
+7.0	28.04878048780488	21.951219512195124	30.48780487804878	19.51219512195122	0.0
+8.0	23.170731707317074	18.29268292682927	39.02439024390244	19.51219512195122	0.0
+9.0	28.04878048780488	29.268292682926827	24.390243902439025	18.29268292682927	0.0
+10.0	24.390243902439025	23.170731707317074	34.146341463414636	18.29268292682927	0.0
+11.0	19.51219512195122	31.70731707317073	28.04878048780488	20.73170731707317	0.0
+12.0	34.146341463414636	23.170731707317074	28.04878048780488	14.634146341463413	0.0
+13.0	26.82926829268293	18.29268292682927	36.58536585365854	18.29268292682927	0.0
+14.0	24.390243902439025	26.82926829268293	29.268292682926827	19.51219512195122	0.0
+15.0	29.268292682926827	21.951219512195124	28.04878048780488	20.73170731707317	0.0
+16.0	31.70731707317073	25.609756097560975	29.268292682926827	13.414634146341465	0.0
+17.0	15.853658536585366	25.609756097560975	35.36585365853659	23.170731707317074	0.0
+18.0	31.70731707317073	17.073170731707318	31.70731707317073	19.51219512195122	0.0
+19.0	24.390243902439025	29.268292682926827	29.268292682926827	17.073170731707318	0.0
+20.0	21.951219512195124	25.609756097560975	29.268292682926827	23.170731707317074	0.0
+21.0	23.170731707317074	28.04878048780488	36.58536585365854	12.195121951219512	0.0
+22.0	28.04878048780488	30.48780487804878	18.29268292682927	23.170731707317074	0.0
+23.0	23.170731707317074	18.29268292682927	29.268292682926827	29.268292682926827	0.0
+24.0	25.609756097560975	19.51219512195122	35.36585365853659	19.51219512195122	0.0
+25.0	23.170731707317074	26.82926829268293	25.609756097560975	24.390243902439025	0.0
+26.0	21.951219512195124	19.51219512195122	41.46341463414634	17.073170731707318	0.0
+27.0	18.29268292682927	29.268292682926827	35.36585365853659	17.073170731707318	0.0
+28.0	29.268292682926827	30.48780487804878	25.609756097560975	14.634146341463413	0.0
+29.0	17.073170731707318	25.609756097560975	36.58536585365854	20.73170731707317	0.0
+30.0	25.609756097560975	21.951219512195124	32.926829268292686	19.51219512195122	0.0
+31.0	29.268292682926827	23.170731707317074	32.926829268292686	14.634146341463413	0.0
+32.0	29.268292682926827	21.951219512195124	24.390243902439025	24.390243902439025	0.0
+33.0	20.73170731707317	31.70731707317073	26.82926829268293	20.73170731707317	0.0
+34.0	18.29268292682927	20.73170731707317	40.243902439024396	20.73170731707317	0.0
+35.0	37.80487804878049	13.414634146341465	28.04878048780488	20.73170731707317	0.0
+36.0	28.04878048780488	28.04878048780488	28.04878048780488	15.853658536585366	0.0
+37.0	21.951219512195124	20.73170731707317	39.02439024390244	18.29268292682927	0.0
+38.0	34.146341463414636	26.82926829268293	14.634146341463413	24.390243902439025	0.0
+39.0	31.70731707317073	17.073170731707318	26.82926829268293	24.390243902439025	0.0
+40.0	26.82926829268293	24.390243902439025	31.70731707317073	17.073170731707318	0.0
+41.0	30.48780487804878	19.51219512195122	25.609756097560975	24.390243902439025	0.0
+42.0	15.853658536585366	25.609756097560975	34.146341463414636	24.390243902439025	0.0
+43.0	29.268292682926827	24.390243902439025	28.04878048780488	18.29268292682927	0.0
+44.0	26.82926829268293	24.390243902439025	31.70731707317073	17.073170731707318	0.0
+45.0	29.268292682926827	23.170731707317074	29.268292682926827	18.29268292682927	0.0
+46.0	24.390243902439025	23.170731707317074	30.48780487804878	21.951219512195124	0.0
+47.0	25.609756097560975	28.04878048780488	30.48780487804878	15.853658536585366	0.0
+48.0	29.268292682926827	25.609756097560975	29.268292682926827	15.853658536585366	0.0
+49.0	23.170731707317074	23.170731707317074	32.926829268292686	20.73170731707317	0.0
+50.0	24.390243902439025	28.04878048780488	31.70731707317073	15.853658536585366	0.0
+51.0	24.390243902439025	24.390243902439025	31.70731707317073	19.51219512195122	0.0
+52.0	18.29268292682927	26.82926829268293	34.146341463414636	20.73170731707317	0.0
+53.0	26.82926829268293	23.170731707317074	36.58536585365854	13.414634146341465	0.0
+54.0	26.82926829268293	23.170731707317074	31.70731707317073	18.29268292682927	0.0
+55.0	25.609756097560975	26.82926829268293	28.04878048780488	19.51219512195122	0.0
+56.0	10.975609756097562	32.926829268292686	40.243902439024396	15.853658536585366	0.0
+57.0	26.82926829268293	19.51219512195122	29.268292682926827	24.390243902439025	0.0
+58.0	26.82926829268293	30.48780487804878	25.609756097560975	17.073170731707318	0.0
+59.0	21.951219512195124	19.51219512195122	32.926829268292686	25.609756097560975	0.0
+60.0	20.73170731707317	28.04878048780488	32.926829268292686	18.29268292682927	0.0
+61.0	30.48780487804878	19.51219512195122	32.926829268292686	17.073170731707318	0.0
+62.0	24.390243902439025	23.170731707317074	30.48780487804878	21.951219512195124	0.0
+63.0	19.51219512195122	23.170731707317074	29.268292682926827	28.04878048780488	0.0
+64.0	25.609756097560975	31.70731707317073	24.390243902439025	18.29268292682927	0.0
+65.0	18.29268292682927	24.390243902439025	30.48780487804878	26.82926829268293	0.0
+66.0	20.73170731707317	19.51219512195122	36.58536585365854	23.170731707317074	0.0
+67.0	23.170731707317074	31.70731707317073	25.609756097560975	19.51219512195122	0.0
+68.0	15.853658536585366	24.390243902439025	42.68292682926829	17.073170731707318	0.0
+69.0	25.609756097560975	26.82926829268293	29.268292682926827	18.29268292682927	0.0
+70.0	24.390243902439025	34.146341463414636	31.70731707317073	9.75609756097561	0.0
+71.0	19.753086419753085	27.160493827160494	29.629629629629626	23.456790123456788	0.0
+72.0	25.0	37.5	17.5	20.0	0.0
+73.0	24.050632911392405	20.253164556962027	34.177215189873415	21.518987341772153	0.0
+74.0	17.56756756756757	31.08108108108108	28.37837837837838	22.972972972972975	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapping_quality_across_reference.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,326 @@
+#Position (bp)	mapping quality
+1.5	0.0
+3.5	0.0
+5.5	0.0
+7.5	0.0
+9.5	0.0
+11.5	0.0
+13.5	0.0
+15.5	0.0
+17.5	0.0
+19.5	0.0
+21.5	0.0
+23.5	0.0
+25.5	0.0
+27.5	0.0
+29.5	0.0
+31.5	0.0
+33.5	0.0
+35.5	0.0
+37.5	0.0
+39.5	0.0
+41.5	0.0
+43.5	0.0
+45.5	0.0
+47.5	0.0
+49.5	0.0
+51.5	0.0
+53.5	255.0
+55.5	255.0
+57.5	255.0
+59.5	255.0
+61.5	255.0
+63.5	255.0
+65.5	255.0
+67.5	255.0
+69.5	255.0
+71.5	255.0
+73.5	255.0
+75.5	255.0
+77.5	255.0
+79.5	255.0
+81.5	255.0
+83.5	255.0
+85.5	255.0
+87.5	255.0
+89.5	255.0
+91.5	236.33333333333334
+93.5	238.2
+95.5	239.72727272727272
+97.5	240.6
+99.5	241.0
+101.5	243.27906976744185
+103.5	244.04347826086956
+105.5	244.27659574468086
+107.5	244.92
+109.5	244.92
+111.5	244.92
+113.5	244.92
+115.5	245.30769230769232
+117.5	245.30769230769232
+119.5	245.30769230769232
+121.5	245.49056603773585
+123.5	246.31034482758622
+125.5	247.125
+127.5	247.36363636363637
+129.5	247.24615384615385
+131.5	247.24615384615385
+133.5	247.125
+135.5	247.47761194029852
+137.5	247.36363636363637
+139.5	247.58823529411765
+141.5	248.0
+143.5	248.28
+145.5	248.3684210526316
+147.5	248.3684210526316
+149.5	248.3684210526316
+151.5	248.3684210526316
+153.5	248.0
+155.5	248.1891891891892
+157.5	248.0958904109589
+159.5	248.0958904109589
+161.5	248.0958904109589
+163.5	247.90140845070422
+165.5	251.54794520547946
+167.5	255.0
+169.5	255.0
+171.5	255.0
+173.5	255.0
+175.5	255.0
+177.5	255.0
+179.5	255.0
+181.5	255.0
+183.5	255.0
+185.5	255.0
+187.5	255.0
+189.5	255.0
+191.5	255.0
+193.5	255.0
+195.5	255.0
+197.5	255.0
+199.5	255.0
+201.5	255.0
+203.5	255.0
+205.5	255.0
+207.5	255.0
+209.5	255.0
+211.5	255.0
+213.5	255.0
+215.5	255.0
+217.5	255.0
+219.5	255.0
+221.5	255.0
+223.5	255.0
+225.5	255.0
+227.5	255.0
+229.5	255.0
+231.5	255.0
+233.5	255.0
+235.5	255.0
+237.5	255.0
+239.5	255.0
+241.5	255.0
+243.5	255.0
+245.5	255.0
+247.5	255.0
+249.5	255.0
+251.5	0.0
+253.5	0.0
+255.5	0.0
+257.5	0.0
+259.5	0.0
+261.5	0.0
+263.5	0.0
+265.5	0.0
+267.5	0.0
+269.5	0.0
+271.5	0.0
+273.5	0.0
+275.5	0.0
+277.5	0.0
+279.5	0.0
+281.5	0.0
+283.5	0.0
+285.5	0.0
+287.5	0.0
+289.5	0.0
+291.5	0.0
+293.5	0.0
+295.5	0.0
+297.5	0.0
+299.5	0.0
+301.5	0.0
+303.5	0.0
+305.5	0.0
+307.5	0.0
+309.5	0.0
+311.5	0.0
+313.5	0.0
+315.5	0.0
+317.5	0.0
+319.5	0.0
+321.5	0.0
+323.5	0.0
+325.5	0.0
+327.5	0.0
+329.5	0.0
+331.5	0.0
+333.5	0.0
+335.5	0.0
+337.5	0.0
+339.5	0.0
+341.5	0.0
+343.5	0.0
+345.5	0.0
+347.5	0.0
+349.5	0.0
+351.5	0.0
+353.5	0.0
+355.5	0.0
+357.5	0.0
+359.5	0.0
+361.5	0.0
+363.5	0.0
+365.5	0.0
+367.5	0.0
+369.5	0.0
+371.5	0.0
+373.5	0.0
+375.5	0.0
+377.5	0.0
+379.5	0.0
+381.5	0.0
+383.5	0.0
+385.5	0.0
+387.5	0.0
+389.5	0.0
+391.5	0.0
+393.5	0.0
+395.5	0.0
+397.5	0.0
+399.5	0.0
+401.5	0.0
+403.5	0.0
+405.5	0.0
+407.5	0.0
+409.5	0.0
+411.5	0.0
+413.5	0.0
+415.5	0.0
+417.5	0.0
+419.5	0.0
+421.5	0.0
+423.5	0.0
+425.5	0.0
+427.5	0.0
+429.5	0.0
+431.5	0.0
+433.5	0.0
+435.5	0.0
+437.5	0.0
+439.5	0.0
+441.5	0.0
+443.5	0.0
+445.5	0.0
+447.5	0.0
+449.5	0.0
+451.5	0.0
+453.5	0.0
+455.5	0.0
+457.5	0.0
+459.5	0.0
+461.5	0.0
+463.5	0.0
+465.5	0.0
+467.5	0.0
+469.5	0.0
+471.5	0.0
+473.5	0.0
+475.5	0.0
+477.5	0.0
+479.5	0.0
+481.5	0.0
+483.5	0.0
+485.5	0.0
+487.5	0.0
+489.5	0.0
+491.5	0.0
+493.5	0.0
+495.5	0.0
+497.5	0.0
+499.5	0.0
+501.5	0.0
+503.5	0.0
+505.5	0.0
+507.5	0.0
+509.5	0.0
+511.5	0.0
+513.5	0.0
+515.5	0.0
+517.5	0.0
+519.5	0.0
+521.5	0.0
+523.5	0.0
+525.5	0.0
+527.5	0.0
+529.5	0.0
+531.5	0.0
+533.5	0.0
+535.5	0.0
+537.5	0.0
+539.5	0.0
+541.5	0.0
+543.5	0.0
+545.5	0.0
+547.5	0.0
+549.5	0.0
+551.5	0.0
+553.5	0.0
+555.5	0.0
+557.5	0.0
+559.5	0.0
+561.5	0.0
+563.5	0.0
+565.5	0.0
+567.5	0.0
+569.5	0.0
+571.5	0.0
+573.5	0.0
+575.5	0.0
+577.5	0.0
+579.5	0.0
+581.5	0.0
+583.5	0.0
+585.5	0.0
+587.5	0.0
+589.5	0.0
+591.5	0.0
+593.5	0.0
+595.5	0.0
+597.5	0.0
+599.5	0.0
+601.5	0.0
+603.5	0.0
+605.5	0.0
+607.5	0.0
+609.5	0.0
+611.5	0.0
+613.5	0.0
+615.5	0.0
+617.5	0.0
+619.5	0.0
+621.5	0.0
+623.5	0.0
+625.5	0.0
+627.5	0.0
+629.5	0.0
+631.5	0.0
+633.5	0.0
+635.5	0.0
+637.5	0.0
+639.5	0.0
+641.5	0.0
+643.5	0.0
+645.5	0.0
+647.5	0.0
+649.5	0.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mapping_quality_histogram.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,13 @@
+#Mapping quality	mapping quality
+235.0	1.0
+237.0	2.0
+239.0	2.0
+240.0	2.0
+241.0	3.0
+243.0	2.0
+244.0	12.0
+245.0	8.0
+246.0	2.0
+247.0	18.0
+248.0	23.0
+255.0	123.0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mouse_counts_ensemble_1000_6.tsv	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,1000 @@
+#gene	-GlcN01	-GlcN02	-GlcN03	+GlcN01	+GlcN02	+GlcN03
+ENSMUSG00000085214	641	542	776	491	791	368
+ENSMUSG00000096956	73	17	47	32	29	63
+ENSMUSG00000021252	2359	1563	2497	2126	2149	1296
+ENSMUSG00000046840	39	165	124	83	144	31
+ENSMUSG00000044062	1	0	3	6	1	0
+ENSMUSG00000007777	292	184	220	228	237	270
+ENSMUSG00000037361	421	300	380	316	393	310
+ENSMUSG00000043644	16	5	7	6	6	8
+ENSMUSG00000024442	812	566	727	569	784	692
+ENSMUSG00000042208	445	273	375	305	410	399
+ENSMUSG00000020831	5	4	5	6	6	3
+ENSMUSG00000025731	1259	942	1113	888	1585	1076
+ENSMUSG00000096232	394	309	396	261	417	306
+ENSMUSG00000055312	53	53	59	43	63	35
+ENSMUSG00000058706	948	581	835	716	927	622
+ENSMUSG00000001418	1440	813	1052	1092	1044	1168
+ENSMUSG00000028608	305	208	262	229	273	225
+ENSMUSG00000089900	3	3	2	7	4	5
+ENSMUSG00000058812	51	30	45	41	32	35
+ENSMUSG00000089889	15	5	21	12	22	9
+ENSMUSG00000087341	82	84	69	145	96	93
+ENSMUSG00000060512	621	495	565	399	691	591
+ENSMUSG00000087361	26	13	20	18	26	10
+ENSMUSG00000051748	5290	4503	5667	8817	5797	1277
+ENSMUSG00000062691	135	92	121	113	141	105
+ENSMUSG00000019689	341	270	361	194	400	200
+ENSMUSG00000071456	38	19	25	22	29	43
+ENSMUSG00000022972	221	148	167	172	215	203
+ENSMUSG00000030663	1070	597	798	671	862	776
+ENSMUSG00000037960	194	88	114	106	114	119
+ENSMUSG00000027637	779	632	672	570	820	868
+ENSMUSG00000029600	6	3	1	6	1	5
+ENSMUSG00000021023	249	234	221	184	237	194
+ENSMUSG00000039195	163	90	166	216	145	199
+ENSMUSG00000045237	267	222	288	198	217	183
+ENSMUSG00000028441	0	0	0	0	0	0
+ENSMUSG00000097616	41	27	32	33	33	48
+ENSMUSG00000097047	12	15	23	9	12	13
+ENSMUSG00000085972	24	7	25	19	25	104
+ENSMUSG00000037971	480	419	491	343	577	361
+ENSMUSG00000046999	0	0	1	1	0	0
+ENSMUSG00000044991	176	58	126	103	123	256
+ENSMUSG00000086191	5	3	4	2	6	2
+ENSMUSG00000097036	0	0	0	0	0	0
+ENSMUSG00000040720	807	491	596	568	621	542
+ENSMUSG00000092203	75	46	59	28	40	65
+ENSMUSG00000063236	196	91	125	110	129	127
+ENSMUSG00000085457	10	5	8	9	4	4
+ENSMUSG00000040591	52	34	59	39	39	24
+ENSMUSG00000097867	125	152	200	139	205	82
+ENSMUSG00000037669	63	43	39	35	45	45
+ENSMUSG00000026154	298	233	285	231	296	211
+ENSMUSG00000035171	488	227	316	257	378	300
+ENSMUSG00000032551	328	126	195	153	278	192
+ENSMUSG00000037086	0	0	0	0	0	1
+ENSMUSG00000078570	129	50	72	44	86	109
+ENSMUSG00000045414	1179	854	813	640	1108	894
+ENSMUSG00000096537	0	0	0	0	0	0
+ENSMUSG00000043687	72	59	69	42	80	64
+ENSMUSG00000063320	47	29	43	25	43	29
+ENSMUSG00000020783	491	222	312	300	407	381
+ENSMUSG00000097290	253	122	210	126	150	160
+ENSMUSG00000028327	2650	1496	2279	2932	2340	1618
+ENSMUSG00000087382	433	112	307	114	140	121
+ENSMUSG00000033688	11175	8162	11448	9133	11522	6616
+ENSMUSG00000087264	1	0	0	0	0	0
+ENSMUSG00000068099	0	0	0	0	0	0
+ENSMUSG00000087651	1	1	0	0	0	0
+ENSMUSG00000072694	58	13	20	26	15	17
+ENSMUSG00000051319	186	177	170	164	149	229
+ENSMUSG00000074578	356	143	234	122	179	142
+ENSMUSG00000097247	0	0	0	0	0	0
+ENSMUSG00000094732	0	2	1	0	2	0
+ENSMUSG00000026051	1	0	0	1	1	1
+ENSMUSG00000087211	0	0	0	0	0	0
+ENSMUSG00000087579	62	81	134	28	343	91
+ENSMUSG00000086899	1	0	0	0	0	0
+ENSMUSG00000024118	1225	363	383	459	2160	664
+ENSMUSG00000035595	61	46	59	59	54	39
+ENSMUSG00000050088	51	20	29	24	37	42
+ENSMUSG00000054676	321	178	294	187	249	260
+ENSMUSG00000094690	0	0	0	0	0	0
+ENSMUSG00000035491	0	1	1	0	0	0
+ENSMUSG00000029813	0	0	0	0	0	0
+ENSMUSG00000025500	54	15	39	44	28	36
+ENSMUSG00000097048	22	17	11	12	23	23
+ENSMUSG00000085114	0	0	0	0	0	0
+ENSMUSG00000032068	95	33	60	58	83	32
+ENSMUSG00000046242	1	0	1	1	1	0
+ENSMUSG00000057818	0	0	1	0	1	1
+ENSMUSG00000029182	0	0	0	0	0	0
+ENSMUSG00000047150	71	57	82	58	79	34
+ENSMUSG00000095384	0	0	0	0	0	0
+ENSMUSG00000085984	1	0	0	0	0	0
+ENSMUSG00000044744	1	1	1	1	1	4
+ENSMUSG00000095040	1	0	0	0	0	0
+ENSMUSG00000056508	2	0	1	1	2	0
+ENSMUSG00000075511	369	208	462	271	474	273
+ENSMUSG00000021534	2	0	1	0	1	0
+ENSMUSG00000044320	2	0	0	0	1	0
+ENSMUSG00000018543	0	0	0	0	0	1
+ENSMUSG00000085944	8	3	5	2	2	2
+ENSMUSG00000030030	19	21	24	19	30	10
+ENSMUSG00000038523	14	1	1	1	2	9
+ENSMUSG00000086327	30	17	16	15	12	20
+ENSMUSG00000085831	0	0	0	0	0	0
+ENSMUSG00000087621	0	0	0	0	0	0
+ENSMUSG00000039174	0	0	0	0	0	0
+ENSMUSG00000028294	0	0	0	0	0	0
+ENSMUSG00000085389	0	0	0	0	0	0
+ENSMUSG00000027973	0	0	0	0	0	0
+ENSMUSG00000010841	0	0	0	0	0	0
+ENSMUSG00000031620	0	0	0	0	0	0
+ENSMUSG00000057816	0	1	0	1	0	0
+ENSMUSG00000086330	15	7	7	11	9	4
+ENSMUSG00000030858	0	0	0	0	0	0
+ENSMUSG00000026831	1	0	0	1	0	6
+ENSMUSG00000097318	20	12	21	23	19	24
+ENSMUSG00000089730	1	0	0	1	2	1
+ENSMUSG00000020270	0	0	0	0	0	0
+ENSMUSG00000056018	0	0	0	0	0	0
+ENSMUSG00000058252	2	0	0	0	1	1
+ENSMUSG00000008028	0	0	2	1	0	1
+ENSMUSG00000069118	0	0	0	0	0	0
+ENSMUSG00000096573	4	0	0	0	1	1
+ENSMUSG00000028287	0	0	0	0	0	0
+ENSMUSG00000026649	36	31	30	35	25	28
+ENSMUSG00000057047	0	0	0	0	0	0
+ENSMUSG00000071721	0	0	0	0	0	0
+ENSMUSG00000023873	14	3	6	10	8	3
+ENSMUSG00000092599	0	0	0	0	0	0
+ENSMUSG00000063971	1	0	0	0	0	0
+ENSMUSG00000036557	0	0	0	0	0	0
+ENSMUSG00000021850	40	10	11	12	27	12
+ENSMUSG00000058925	2	0	0	0	0	0
+ENSMUSG00000063714	44	23	38	22	36	14
+ENSMUSG00000031682	0	0	3	1	0	0
+ENSMUSG00000079476	0	0	0	0	0	0
+ENSMUSG00000029766	0	0	0	0	0	0
+ENSMUSG00000020617	0	0	0	0	0	0
+ENSMUSG00000031927	0	0	0	0	0	0
+ENSMUSG00000079179	204	146	187	126	179	122
+ENSMUSG00000096571	0	0	0	0	0	0
+ENSMUSG00000028589	0	0	0	0	0	0
+ENSMUSG00000079346	0	0	0	0	0	0
+ENSMUSG00000027886	0	0	1	0	0	0
+ENSMUSG00000085260	0	0	2	1	0	0
+ENSMUSG00000041399	0	0	0	0	0	0
+ENSMUSG00000054727	0	0	0	0	0	0
+ENSMUSG00000042800	4	2	2	1	1	0
+ENSMUSG00000079666	0	0	0	0	0	0
+ENSMUSG00000094445	0	0	0	0	0	0
+ENSMUSG00000015962	1	0	0	0	0	1
+ENSMUSG00000031509	0	0	0	0	1	1
+ENSMUSG00000029320	0	0	0	0	0	0
+ENSMUSG00000053783	0	0	0	0	1	1
+ENSMUSG00000032300	349	112	164	162	195	312
+ENSMUSG00000024729	0	0	0	0	0	0
+ENSMUSG00000037884	0	0	0	0	0	0
+ENSMUSG00000086348	0	0	0	0	0	0
+ENSMUSG00000056912	0	0	0	0	0	0
+ENSMUSG00000038408	0	0	0	0	0	0
+ENSMUSG00000033993	0	0	0	0	0	0
+ENSMUSG00000031809	0	0	0	0	0	0
+ENSMUSG00000037910	0	0	0	0	0	0
+ENSMUSG00000058935	0	0	0	0	0	0
+ENSMUSG00000029620	0	0	0	0	0	0
+ENSMUSG00000060715	0	0	0	0	2	0
+ENSMUSG00000040340	0	1	0	0	2	0
+ENSMUSG00000085757	0	0	0	0	0	0
+ENSMUSG00000043629	2	0	2	0	0	1
+ENSMUSG00000086202	0	0	0	0	0	0
+ENSMUSG00000068299	128	87	144	82	113	100
+ENSMUSG00000085416	0	0	0	0	0	0
+ENSMUSG00000038987	9	3	4	6	1	4
+ENSMUSG00000059695	0	0	0	0	0	0
+ENSMUSG00000026931	0	0	0	0	0	0
+ENSMUSG00000036574	0	0	0	0	0	0
+ENSMUSG00000027409	0	0	0	0	0	0
+ENSMUSG00000085438	59	35	30	32	50	51
+ENSMUSG00000035085	2	0	1	4	2	4
+ENSMUSG00000050844	0	1	1	1	0	0
+ENSMUSG00000059690	0	0	0	0	0	0
+ENSMUSG00000019797	298	227	276	202	324	239
+ENSMUSG00000027518	0	0	0	0	0	0
+ENSMUSG00000035629	5	2	5	3	5	4
+ENSMUSG00000087343	0	0	0	0	0	0
+ENSMUSG00000038165	0	0	0	0	0	0
+ENSMUSG00000028451	0	0	0	0	0	0
+ENSMUSG00000057072	1	0	1	1	4	0
+ENSMUSG00000087393	0	0	0	0	0	0
+ENSMUSG00000029248	0	0	0	0	0	0
+ENSMUSG00000020940	0	0	0	0	0	0
+ENSMUSG00000045709	0	0	0	0	0	0
+ENSMUSG00000072473	0	0	0	0	0	0
+ENSMUSG00000086186	0	0	0	0	0	0
+ENSMUSG00000045022	0	0	1	0	0	0
+ENSMUSG00000078612	413	62	147	176	130	239
+ENSMUSG00000078935	0	0	0	0	0	0
+ENSMUSG00000024728	0	0	0	0	0	0
+ENSMUSG00000032666	184	94	118	121	123	81
+ENSMUSG00000011154	0	0	0	0	0	0
+ENSMUSG00000086379	0	0	0	0	0	0
+ENSMUSG00000026809	7	1	3	3	0	1
+ENSMUSG00000097321	20	12	24	11	16	45
+ENSMUSG00000056821	1	1	0	0	0	1
+ENSMUSG00000038782	2	1	4	4	2	3
+ENSMUSG00000089798	9	4	8	1	5	3
+ENSMUSG00000033053	0	0	0	0	0	0
+ENSMUSG00000086823	0	0	0	0	0	0
+ENSMUSG00000052075	0	0	0	0	0	0
+ENSMUSG00000031452	0	0	1	0	0	0
+ENSMUSG00000044916	1	1	2	2	6	3
+ENSMUSG00000071103	34	22	30	16	34	29
+ENSMUSG00000086788	0	0	0	0	0	0
+ENSMUSG00000098144	1	0	0	0	0	0
+ENSMUSG00000061633	0	0	0	0	0	0
+ENSMUSG00000085333	0	0	0	1	0	0
+ENSMUSG00000091071	43	15	26	9	19	33
+ENSMUSG00000031847	9	4	5	2	9	5
+ENSMUSG00000052794	97	59	63	62	76	83
+ENSMUSG00000097424	0	0	0	0	0	0
+ENSMUSG00000092239	0	0	0	0	0	0
+ENSMUSG00000032894	0	0	0	0	0	0
+ENSMUSG00000024532	0	0	0	0	0	0
+ENSMUSG00000097962	0	0	0	0	0	0
+ENSMUSG00000055833	8	7	14	9	7	11
+ENSMUSG00000074619	1	0	1	0	0	0
+ENSMUSG00000040163	0	0	0	0	0	0
+ENSMUSG00000029867	0	0	0	0	0	0
+ENSMUSG00000097893	26	18	13	19	23	22
+ENSMUSG00000005983	16	5	14	11	9	11
+ENSMUSG00000027327	123	86	100	81	110	118
+ENSMUSG00000070568	2	0	0	0	0	0
+ENSMUSG00000092369	0	0	0	0	0	0
+ENSMUSG00000019945	71	67	80	43	84	29
+ENSMUSG00000086999	0	0	0	0	0	0
+ENSMUSG00000057402	0	0	0	0	0	0
+ENSMUSG00000078593	0	0	0	0	0	0
+ENSMUSG00000087044	0	0	0	0	0	0
+ENSMUSG00000086391	2	0	0	0	0	0
+ENSMUSG00000078492	8	3	3	3	7	1
+ENSMUSG00000085561	0	0	0	0	0	0
+ENSMUSG00000094103	0	0	0	0	0	0
+ENSMUSG00000043773	17	20	20	12	30	11
+ENSMUSG00000085077	0	0	0	0	0	1
+ENSMUSG00000070709	84	45	76	64	60	46
+ENSMUSG00000043859	0	0	0	0	0	0
+ENSMUSG00000086951	3	0	0	4	0	0
+ENSMUSG00000061759	293	185	174	245	326	310
+ENSMUSG00000085889	4	0	0	0	0	1
+ENSMUSG00000040456	1	1	0	1	0	0
+ENSMUSG00000093616	0	0	0	0	0	0
+ENSMUSG00000037263	11	58	149	123	3	3
+ENSMUSG00000044854	19	8	13	14	7	7
+ENSMUSG00000074139	0	0	0	0	0	0
+ENSMUSG00000084757	0	0	0	0	0	0
+ENSMUSG00000020164	0	0	1	0	0	0
+ENSMUSG00000086887	0	0	0	2	0	0
+ENSMUSG00000078957	0	0	1	0	0	0
+ENSMUSG00000085580	0	0	0	0	0	0
+ENSMUSG00000024209	4	2	0	1	0	1
+ENSMUSG00000028009	3	13	5	4	9	5
+ENSMUSG00000096655	2	0	2	1	2	1
+ENSMUSG00000032900	0	0	0	0	0	0
+ENSMUSG00000073598	5	0	0	4	0	1
+ENSMUSG00000036162	51	23	28	28	22	20
+ENSMUSG00000038323	442	255	299	303	514	403
+ENSMUSG00000085800	0	0	0	0	0	0
+ENSMUSG00000046408	4	6	1	4	6	4
+ENSMUSG00000021545	0	0	0	0	1	0
+ENSMUSG00000042184	0	0	0	0	0	0
+ENSMUSG00000080980	0	0	0	0	0	0
+ENSMUSG00000090307	25	8	17	20	7	7
+ENSMUSG00000087204	0	0	0	0	0	0
+ENSMUSG00000029883	0	0	0	0	0	0
+ENSMUSG00000032566	0	0	0	0	0	0
+ENSMUSG00000084859	0	0	0	0	0	0
+ENSMUSG00000031118	0	0	0	0	0	0
+ENSMUSG00000085265	0	0	0	0	0	0
+ENSMUSG00000070532	9	0	2	0	3	8
+ENSMUSG00000052222	5	1	5	1	2	3
+ENSMUSG00000058101	0	0	0	0	0	0
+ENSMUSG00000087104	0	0	0	0	0	0
+ENSMUSG00000071265	0	0	0	0	0	0
+ENSMUSG00000097080	31	22	26	14	18	12
+ENSMUSG00000033029	45	29	34	23	46	41
+ENSMUSG00000086128	2	1	0	0	4	1
+ENSMUSG00000086781	0	0	0	0	0	0
+ENSMUSG00000092499	11	15	10	4	18	5
+ENSMUSG00000084811	0	0	0	0	0	0
+ENSMUSG00000078600	0	0	0	0	0	0
+ENSMUSG00000090840	0	1	0	1	1	0
+ENSMUSG00000020286	0	0	0	0	0	0
+ENSMUSG00000078667	97	61	73	57	80	70
+ENSMUSG00000086046	0	0	0	0	0	0
+ENSMUSG00000098230	0	0	0	0	0	0
+ENSMUSG00000074346	0	0	0	0	0	0
+ENSMUSG00000079502	4	2	8	5	3	2
+ENSMUSG00000097675	18	19	26	10	24	19
+ENSMUSG00000032611	2	5	0	0	14	8
+ENSMUSG00000074343	0	0	0	0	0	0
+ENSMUSG00000034031	0	0	0	0	0	0
+ENSMUSG00000052371	0	0	0	0	0	0
+ENSMUSG00000085044	0	0	0	0	0	0
+ENSMUSG00000008307	19	5	11	8	8	12
+ENSMUSG00000079407	0	0	0	0	0	0
+ENSMUSG00000087047	4	1	1	4	2	1
+ENSMUSG00000042888	0	0	0	0	0	0
+ENSMUSG00000063458	43	22	35	49	15	61
+ENSMUSG00000096935	93	62	95	66	96	89
+ENSMUSG00000047129	1	0	1	0	1	0
+ENSMUSG00000086333	0	0	0	0	0	0
+ENSMUSG00000092066	0	0	0	0	0	0
+ENSMUSG00000094928	0	0	0	0	0	0
+ENSMUSG00000024786	1	0	1	1	0	1
+ENSMUSG00000029526	0	0	0	0	0	0
+ENSMUSG00000072878	0	0	0	1	0	0
+ENSMUSG00000085614	7	1	0	1	2	0
+ENSMUSG00000086080	0	0	0	0	0	0
+ENSMUSG00000040822	438	271	352	333	370	310
+ENSMUSG00000085263	0	0	0	0	0	0
+ENSMUSG00000097584	0	0	0	0	0	0
+ENSMUSG00000085197	1	0	0	0	0	0
+ENSMUSG00000018479	0	1	0	0	0	0
+ENSMUSG00000031998	2	0	2	0	0	0
+ENSMUSG00000021977	0	0	0	0	0	0
+ENSMUSG00000086550	0	0	0	0	0	0
+ENSMUSG00000071653	271	169	239	209	201	215
+ENSMUSG00000094808	0	0	0	0	0	0
+ENSMUSG00000078607	114	38	110	62	83	37
+ENSMUSG00000041707	109	23	40	56	25	27
+ENSMUSG00000056313	655	508	337	514	846	280
+ENSMUSG00000022507	827	430	671	669	618	973
+ENSMUSG00000097412	46	35	50	31	52	37
+ENSMUSG00000086390	46	34	40	48	30	20
+ENSMUSG00000037600	3	1	0	1	1	1
+ENSMUSG00000089997	2	1	1	0	2	1
+ENSMUSG00000087331	28	18	24	23	32	9
+ENSMUSG00000078784	425	242	310	287	371	370
+ENSMUSG00000044145	13	5	6	6	14	6
+ENSMUSG00000048429	873	650	688	675	927	832
+ENSMUSG00000044148	369	143	245	176	196	215
+ENSMUSG00000020812	34	16	15	13	20	15
+ENSMUSG00000013974	17	4	12	22	1	4
+ENSMUSG00000097101	143	98	147	103	89	121
+ENSMUSG00000086818	6	0	2	1	3	1
+ENSMUSG00000054091	431	230	301	261	267	319
+ENSMUSG00000062760	6	3	4	25	8	0
+ENSMUSG00000020284	176	72	143	104	114	107
+ENSMUSG00000078572	193	156	225	177	193	152
+ENSMUSG00000036027	52	81	157	68	118	6
+ENSMUSG00000035372	1324	371	687	303	750	758
+ENSMUSG00000073155	357	389	396	267	438	536
+ENSMUSG00000027713	24	8	14	10	12	13
+ENSMUSG00000084925	9	2	6	4	6	5
+ENSMUSG00000090925	505	48	197	144	177	155
+ENSMUSG00000013653	0	0	0	0	0	0
+ENSMUSG00000039339	4	3	0	1	3	4
+ENSMUSG00000085042	16	14	6	7	12	7
+ENSMUSG00000067297	9	1	4	3	2	3
+ENSMUSG00000042041	517	118	212	369	153	971
+ENSMUSG00000028407	79	88	100	71	116	57
+ENSMUSG00000095620	0	0	1	0	1	1
+ENSMUSG00000062376	249	147	199	225	221	206
+ENSMUSG00000042233	19	14	27	10	17	12
+ENSMUSG00000091575	25	10	14	3	4	12
+ENSMUSG00000025528	0	0	0	0	0	0
+ENSMUSG00000021290	1313	863	1206	805	1319	945
+ENSMUSG00000029847	6	0	0	0	0	0
+ENSMUSG00000020083	47	20	53	42	27	54
+ENSMUSG00000029384	1	2	2	1	2	2
+ENSMUSG00000063522	11	2	6	8	7	1
+ENSMUSG00000021458	211	118	147	166	197	228
+ENSMUSG00000063018	2	1	2	0	1	3
+ENSMUSG00000026090	17	6	8	4	4	0
+ENSMUSG00000074829	18	16	12	12	11	7
+ENSMUSG00000030587	249	59	120	215	192	344
+ENSMUSG00000013083	0	0	0	0	3	1
+ENSMUSG00000029882	0	0	0	0	0	0
+ENSMUSG00000086316	98	24	49	37	27	50
+ENSMUSG00000083844	153	128	140	93	121	129
+ENSMUSG00000021550	638	374	512	454	536	459
+ENSMUSG00000029559	277	160	229	180	211	194
+ENSMUSG00000035401	315	176	204	178	273	197
+ENSMUSG00000092570	0	0	0	0	0	0
+ENSMUSG00000078439	39	13	31	22	22	48
+ENSMUSG00000078546	48	22	31	32	31	18
+ENSMUSG00000037145	5	0	1	0	2	1
+ENSMUSG00000087380	13	11	12	13	10	19
+ENSMUSG00000071252	58	12	24	32	43	33
+ENSMUSG00000081766	0	0	0	0	0	0
+ENSMUSG00000085394	1	0	0	1	0	0
+ENSMUSG00000086494	24	22	17	32	35	29
+ENSMUSG00000085347	1	1	0	1	0	0
+ENSMUSG00000039269	0	0	0	0	0	0
+ENSMUSG00000078257	0	0	0	0	0	0
+ENSMUSG00000075605	0	0	0	0	0	0
+ENSMUSG00000032403	121	77	121	73	119	101
+ENSMUSG00000097354	59	35	53	46	98	31
+ENSMUSG00000053353	1	2	2	1	5	4
+ENSMUSG00000036731	0	0	0	0	0	0
+ENSMUSG00000028396	0	0	0	0	0	0
+ENSMUSG00000025384	212	110	181	126	133	144
+ENSMUSG00000087254	10	7	13	4	7	1
+ENSMUSG00000046748	0	0	3	0	4	0
+ENSMUSG00000034159	0	0	0	0	0	1
+ENSMUSG00000009210	0	0	1	0	0	2
+ENSMUSG00000079283	57	29	42	27	29	48
+ENSMUSG00000097162	7	7	21	7	13	11
+ENSMUSG00000020133	331	177	299	229	298	275
+ENSMUSG00000033967	23	30	71	52	28	34
+ENSMUSG00000097729	192	66	148	83	91	82
+ENSMUSG00000019933	0	0	0	1	0	0
+ENSMUSG00000049643	51	22	30	24	36	38
+ENSMUSG00000031983	419	258	311	283	440	383
+ENSMUSG00000032062	320	181	253	203	211	244
+ENSMUSG00000020441	210	113	126	122	101	126
+ENSMUSG00000068078	0	0	0	0	0	0
+ENSMUSG00000026319	4	6	8	4	12	2
+ENSMUSG00000041203	650	340	447	440	471	418
+ENSMUSG00000062619	527	328	535	349	564	343
+ENSMUSG00000078486	13	5	9	4	5	3
+ENSMUSG00000090356	0	1	1	4	0	1
+ENSMUSG00000034157	18	33	18	27	45	37
+ENSMUSG00000002345	226	165	194	188	189	168
+ENSMUSG00000045176	204	90	148	201	122	165
+ENSMUSG00000085779	0	0	0	0	0	0
+ENSMUSG00000090314	0	0	0	0	0	0
+ENSMUSG00000015519	0	0	0	0	0	0
+ENSMUSG00000040177	67	36	62	47	47	84
+ENSMUSG00000048830	0	0	0	0	0	0
+ENSMUSG00000050705	424	281	369	228	439	355
+ENSMUSG00000050704	0	0	0	0	0	0
+ENSMUSG00000087410	0	0	0	0	0	0
+ENSMUSG00000020747	1002	828	978	786	914	651
+ENSMUSG00000097102	1	1	5	0	1	0
+ENSMUSG00000045331	0	0	0	0	0	0
+ENSMUSG00000045411	323	147	229	155	216	188
+ENSMUSG00000085860	0	0	0	0	0	0
+ENSMUSG00000036873	78	49	77	80	86	93
+ENSMUSG00000085338	2	0	0	0	0	0
+ENSMUSG00000087590	44	37	52	23	42	20
+ENSMUSG00000071398	0	0	1	0	0	0
+ENSMUSG00000086841	372	154	269	136	161	167
+ENSMUSG00000090470	0	0	0	0	0	0
+ENSMUSG00000049760	1227	796	1071	873	1185	1141
+ENSMUSG00000046791	119	90	89	118	121	96
+ENSMUSG00000038311	0	1	0	2	1	4
+ENSMUSG00000073164	5	2	1	3	7	3
+ENSMUSG00000034173	68	18	76	20	61	33
+ENSMUSG00000086745	0	1	0	1	0	0
+ENSMUSG00000038065	41	18	14	13	21	25
+ENSMUSG00000074269	41	21	7	6	10	23
+ENSMUSG00000097398	0	0	0	0	0	0
+ENSMUSG00000039801	357	113	165	138	231	242
+ENSMUSG00000085824	0	1	3	0	1	0
+ENSMUSG00000051297	0	0	0	1	0	0
+ENSMUSG00000024726	467	277	328	275	401	294
+ENSMUSG00000032840	224	199	197	179	221	195
+ENSMUSG00000086219	28	12	22	17	14	13
+ENSMUSG00000064308	1	0	0	0	0	0
+ENSMUSG00000074832	0	0	0	0	0	0
+ENSMUSG00000073236	32	23	40	36	34	43
+ENSMUSG00000071632	345	190	266	177	480	328
+ENSMUSG00000086438	0	0	0	0	0	0
+ENSMUSG00000036955	340	249	322	253	365	325
+ENSMUSG00000043391	351	183	272	339	185	212
+ENSMUSG00000044496	717	410	523	491	610	485
+ENSMUSG00000068011	468	273	341	465	278	496
+ENSMUSG00000052419	459	227	320	286	313	322
+ENSMUSG00000073684	50	17	42	33	30	24
+ENSMUSG00000031242	617	339	398	370	465	405
+ENSMUSG00000071793	454	265	377	174	375	268
+ENSMUSG00000060301	285	193	270	172	220	161
+ENSMUSG00000022701	160	81	121	87	114	103
+ENSMUSG00000060424	0	0	0	0	0	0
+ENSMUSG00000031112	42	11	14	15	9	13
+ENSMUSG00000093565	19	13	19	17	18	13
+ENSMUSG00000097537	10	1	0	2	2	3
+ENSMUSG00000030924	36	18	14	14	32	13
+ENSMUSG00000085562	1	0	0	0	0	1
+ENSMUSG00000009114	2	0	3	3	0	0
+ENSMUSG00000039043	248	142	181	161	174	186
+ENSMUSG00000024227	0	0	1	0	0	0
+ENSMUSG00000087259	28	5	22	12	12	7
+ENSMUSG00000085555	0	0	0	0	0	0
+ENSMUSG00000097536	1	0	4	1	0	0
+ENSMUSG00000074415	27	7	15	12	15	23
+ENSMUSG00000079671	34	7	14	8	7	15
+ENSMUSG00000054514	4	2	8	3	6	2
+ENSMUSG00000085236	0	1	0	0	0	0
+ENSMUSG00000059482	123	59	77	92	128	65
+ENSMUSG00000066000	62	2	5	0	80	49
+ENSMUSG00000085936	2	0	1	0	1	4
+ENSMUSG00000097040	0	0	0	0	0	2
+ENSMUSG00000049916	3	0	3	4	0	0
+ENSMUSG00000010277	4799	3039	3572	3011	4929	3796
+ENSMUSG00000085882	531	358	503	423	505	366
+ENSMUSG00000092486	33	5	11	11	4	10
+ENSMUSG00000096001	0	0	2	0	1	1
+ENSMUSG00000028536	153	85	155	98	152	71
+ENSMUSG00000038005	217	93	109	108	155	117
+ENSMUSG00000097180	0	0	0	0	2	0
+ENSMUSG00000041789	2	2	1	2	0	1
+ENSMUSG00000097787	23	18	22	10	23	16
+ENSMUSG00000034601	7	1	8	6	3	4
+ENSMUSG00000039990	593	425	498	419	663	447
+ENSMUSG00000021807	1589	887	1142	1047	1420	1258
+ENSMUSG00000024273	123	70	103	90	133	102
+ENSMUSG00000086224	3	3	2	4	0	1
+ENSMUSG00000085763	0	0	0	0	0	0
+ENSMUSG00000053080	128	94	106	79	110	80
+ENSMUSG00000085696	0	0	0	0	0	0
+ENSMUSG00000072704	1763	1391	1589	1094	1824	1464
+ENSMUSG00000076437	17	5	8	13	12	19
+ENSMUSG00000062198	8	6	9	2	4	6
+ENSMUSG00000098090	32	6	4	4	4	13
+ENSMUSG00000087497	45	26	43	31	42	28
+ENSMUSG00000045464	41	16	31	30	36	36
+ENSMUSG00000031984	530	349	435	440	461	402
+ENSMUSG00000047635	139	83	137	112	155	91
+ENSMUSG00000030378	330	202	179	37	995	169
+ENSMUSG00000086859	132	66	84	52	88	69
+ENSMUSG00000097929	0	0	0	0	1	0
+ENSMUSG00000020491	81	56	51	61	61	56
+ENSMUSG00000049881	136	90	62	89	109	102
+ENSMUSG00000096995	8	3	3	4	3	1
+ENSMUSG00000037735	3	0	2	2	1	1
+ENSMUSG00000092574	51	24	29	28	28	36
+ENSMUSG00000090386	8	10	8	7	10	10
+ENSMUSG00000028060	1119	640	780	555	986	960
+ENSMUSG00000086629	10	6	21	13	15	6
+ENSMUSG00000018570	3	3	4	3	2	0
+ENSMUSG00000087213	45	3	6	7	19	27
+ENSMUSG00000039725	110	75	57	84	73	82
+ENSMUSG00000075389	24	32	45	28	34	39
+ENSMUSG00000040204	79	2	22	60	8	33
+ENSMUSG00000058833	426	300	392	280	375	344
+ENSMUSG00000097709	0	0	0	0	0	0
+ENSMUSG00000086283	0	0	0	0	0	1
+ENSMUSG00000087060	3	0	1	5	0	1
+ENSMUSG00000090260	1	1	1	3	1	1
+ENSMUSG00000026227	8	7	8	7	12	11
+ENSMUSG00000091475	10	1	2	0	4	0
+ENSMUSG00000084966	0	0	0	0	0	0
+ENSMUSG00000032712	1019	516	523	383	717	716
+ENSMUSG00000055188	2	1	4	0	0	2
+ENSMUSG00000043833	100	35	101	46	50	46
+ENSMUSG00000087271	7	12	21	13	10	6
+ENSMUSG00000044117	4	3	7	4	15	8
+ENSMUSG00000051339	2367	1258	2398	2502	1759	1790
+ENSMUSG00000054418	2	0	0	2	0	0
+ENSMUSG00000071860	0	0	0	0	0	0
+ENSMUSG00000087403	3	2	3	3	1	2
+ENSMUSG00000073596	0	1	0	0	0	1
+ENSMUSG00000097277	44	16	23	18	28	23
+ENSMUSG00000087038	0	0	0	0	0	0
+ENSMUSG00000030385	0	0	0	0	0	0
+ENSMUSG00000086284	0	0	0	0	0	0
+ENSMUSG00000067833	3770	2005	2385	1886	2500	2574
+ENSMUSG00000070282	16	5	15	8	8	7
+ENSMUSG00000084885	0	1	1	0	0	0
+ENSMUSG00000020381	91	35	64	76	89	77
+ENSMUSG00000086254	0	0	0	0	0	0
+ENSMUSG00000079737	46	36	38	22	44	53
+ENSMUSG00000024410	449	323	399	278	476	448
+ENSMUSG00000079450	10	8	8	4	6	6
+ENSMUSG00000026388	6	3	7	8	4	2
+ENSMUSG00000050604	5	2	1	1	1	4
+ENSMUSG00000094958	27	28	37	21	40	30
+ENSMUSG00000067879	7	2	6	12	4	34
+ENSMUSG00000089922	0	0	0	0	0	0
+ENSMUSG00000025102	216	117	162	125	155	169
+ENSMUSG00000028300	410	129	189	180	247	307
+ENSMUSG00000097503	40	33	47	78	34	32
+ENSMUSG00000090061	9	2	11	3	5	5
+ENSMUSG00000035868	120	153	138	156	144	194
+ENSMUSG00000085622	39	30	32	28	38	35
+ENSMUSG00000037818	290	233	328	160	405	235
+ENSMUSG00000046806	42	11	17	16	21	29
+ENSMUSG00000074635	13	4	8	11	12	3
+ENSMUSG00000026258	0	1	0	0	0	0
+ENSMUSG00000053553	188	25	67	72	115	49
+ENSMUSG00000086815	0	0	0	0	0	0
+ENSMUSG00000085582	0	0	0	0	0	0
+ENSMUSG00000063364	5	4	2	4	4	4
+ENSMUSG00000096965	2	0	0	0	0	0
+ENSMUSG00000071540	0	0	4	1	0	1
+ENSMUSG00000036242	7	0	1	5	5	1
+ENSMUSG00000089759	1	0	3	0	0	0
+ENSMUSG00000031125	0	0	2	0	1	0
+ENSMUSG00000033111	15	19	21	20	22	13
+ENSMUSG00000071181	10	6	10	3	9	3
+ENSMUSG00000031179	0	0	0	0	0	0
+ENSMUSG00000038917	4	4	2	4	2	2
+ENSMUSG00000064202	14	23	12	11	26	10
+ENSMUSG00000048106	318	172	243	183	278	190
+ENSMUSG00000074024	6	5	7	2	3	4
+ENSMUSG00000097184	23	4	17	10	6	13
+ENSMUSG00000020101	10	7	4	7	3	6
+ENSMUSG00000030641	70	8	12	17	13	42
+ENSMUSG00000048699	0	0	0	0	0	0
+ENSMUSG00000053714	17	12	35	10	18	11
+ENSMUSG00000085421	2	0	1	0	0	3
+ENSMUSG00000097350	26	10	18	23	15	15
+ENSMUSG00000097236	70	30	83	23	62	32
+ENSMUSG00000024481	2	0	0	0	0	0
+ENSMUSG00000097697	0	0	0	1	1	0
+ENSMUSG00000086015	8	10	12	10	8	4
+ENSMUSG00000085287	64	36	55	36	41	34
+ENSMUSG00000062822	48	16	29	22	30	32
+ENSMUSG00000074782	59	34	69	28	49	47
+ENSMUSG00000075217	0	0	0	0	0	0
+ENSMUSG00000033342	18	6	15	16	29	7
+ENSMUSG00000092171	2	2	0	3	3	2
+ENSMUSG00000032057	0	0	0	0	0	0
+ENSMUSG00000097074	0	0	0	0	0	0
+ENSMUSG00000025871	54	39	41	31	61	47
+ENSMUSG00000023350	0	0	0	0	0	0
+ENSMUSG00000026734	0	0	0	0	0	0
+ENSMUSG00000027196	11	4	5	3	12	10
+ENSMUSG00000029828	6	4	8	3	4	5
+ENSMUSG00000084980	42	17	31	33	34	27
+ENSMUSG00000027345	0	0	0	0	0	0
+ENSMUSG00000061525	0	0	0	0	0	0
+ENSMUSG00000049815	0	0	0	0	0	0
+ENSMUSG00000040514	0	0	0	0	0	0
+ENSMUSG00000094577	0	0	0	0	0	0
+ENSMUSG00000044544	2	1	0	0	0	0
+ENSMUSG00000098150	1	1	0	0	0	0
+ENSMUSG00000049902	0	0	0	0	0	0
+ENSMUSG00000036934	19	17	15	22	25	32
+ENSMUSG00000039540	0	0	0	0	0	0
+ENSMUSG00000089707	2	0	1	2	1	0
+ENSMUSG00000026940	4	1	4	1	2	3
+ENSMUSG00000086657	19	7	17	11	7	10
+ENSMUSG00000034689	0	0	0	0	0	0
+ENSMUSG00000085704	38	15	28	20	31	20
+ENSMUSG00000020434	1	0	0	0	0	0
+ENSMUSG00000028520	0	0	0	0	0	0
+ENSMUSG00000056919	157	52	60	70	67	110
+ENSMUSG00000042943	0	0	0	0	0	0
+ENSMUSG00000047720	0	0	1	0	0	0
+ENSMUSG00000043429	0	0	0	0	0	0
+ENSMUSG00000085528	0	0	0	0	0	0
+ENSMUSG00000087460	4	0	0	0	0	0
+ENSMUSG00000079421	0	0	0	0	0	0
+ENSMUSG00000027309	820	447	503	459	555	1103
+ENSMUSG00000020332	0	0	1	0	0	0
+ENSMUSG00000087354	14	4	1	4	12	6
+ENSMUSG00000020234	70	29	31	47	38	43
+ENSMUSG00000086638	4	1	5	5	4	6
+ENSMUSG00000085940	0	0	0	0	0	0
+ENSMUSG00000087338	124	90	124	100	87	66
+ENSMUSG00000086923	0	0	0	0	0	0
+ENSMUSG00000075524	0	0	0	0	0	0
+ENSMUSG00000086221	0	0	0	0	0	0
+ENSMUSG00000085558	95	58	81	66	98	46
+ENSMUSG00000025783	0	0	0	0	0	0
+ENSMUSG00000020191	2	0	2	0	0	1
+ENSMUSG00000035387	0	0	0	0	0	0
+ENSMUSG00000022993	0	0	0	1	1	1
+ENSMUSG00000071818	0	0	1	3	1	0
+ENSMUSG00000087625	0	0	0	0	0	0
+ENSMUSG00000051278	100	14	19	16	13	35
+ENSMUSG00000086066	0	0	0	0	0	0
+ENSMUSG00000026736	2	1	0	2	1	3
+ENSMUSG00000037466	53	1	6	21	5	25
+ENSMUSG00000073085	0	0	0	0	0	0
+ENSMUSG00000049507	4	2	3	4	1	2
+ENSMUSG00000086918	7	0	1	1	5	5
+ENSMUSG00000027157	0	0	0	0	0	0
+ENSMUSG00000068046	0	0	0	0	0	0
+ENSMUSG00000046567	77	70	92	78	85	81
+ENSMUSG00000075042	6	4	2	2	3	2
+ENSMUSG00000002240	0	0	0	0	0	0
+ENSMUSG00000008129	0	0	0	0	0	0
+ENSMUSG00000074248	0	0	1	0	0	0
+ENSMUSG00000091692	0	0	0	0	0	0
+ENSMUSG00000042360	4	2	5	1	3	0
+ENSMUSG00000022798	0	0	0	0	0	0
+ENSMUSG00000093472	0	0	0	0	0	0
+ENSMUSG00000085405	0	0	0	0	0	0
+ENSMUSG00000044081	11	8	9	9	10	3
+ENSMUSG00000087609	0	0	0	0	0	0
+ENSMUSG00000087223	3	4	4	4	4	5
+ENSMUSG00000086969	0	0	0	2	0	1
+ENSMUSG00000069712	0	0	1	0	0	0
+ENSMUSG00000097172	0	0	0	0	0	0
+ENSMUSG00000067795	0	0	0	0	0	0
+ENSMUSG00000022288	0	0	0	0	0	0
+ENSMUSG00000021098	0	0	0	0	0	0
+ENSMUSG00000089879	0	0	0	0	0	0
+ENSMUSG00000082843	0	0	0	0	0	0
+ENSMUSG00000022116	0	0	0	0	0	0
+ENSMUSG00000079093	0	0	0	0	0	0
+ENSMUSG00000022759	0	0	0	0	0	0
+ENSMUSG00000045989	0	0	0	0	0	0
+ENSMUSG00000021747	5	1	1	0	2	10
+ENSMUSG00000087358	0	0	0	0	0	0
+ENSMUSG00000059920	412	223	259	311	346	333
+ENSMUSG00000097898	0	0	0	0	0	0
+ENSMUSG00000097553	0	0	0	0	0	0
+ENSMUSG00000080907	48	36	45	20	41	79
+ENSMUSG00000078618	0	0	0	0	0	0
+ENSMUSG00000097651	0	0	0	0	0	1
+ENSMUSG00000087459	0	0	0	0	0	0
+ENSMUSG00000056682	0	0	0	0	0	0
+ENSMUSG00000085641	0	0	0	0	0	0
+ENSMUSG00000097516	0	0	0	0	0	0
+ENSMUSG00000096265	1	0	0	0	1	1
+ENSMUSG00000097370	0	0	0	0	0	0
+ENSMUSG00000079525	0	0	0	0	0	0
+ENSMUSG00000049160	0	0	0	0	0	0
+ENSMUSG00000043583	0	0	0	0	0	0
+ENSMUSG00000091686	0	0	0	0	1	0
+ENSMUSG00000086529	394	342	413	392	410	242
+ENSMUSG00000097693	0	0	0	0	0	0
+ENSMUSG00000060029	3	2	1	0	1	1
+ENSMUSG00000096405	0	0	0	0	0	0
+ENSMUSG00000085238	0	0	1	0	0	2
+ENSMUSG00000035651	0	0	0	0	0	0
+ENSMUSG00000086332	42	25	28	45	56	23
+ENSMUSG00000090160	0	0	0	0	0	0
+ENSMUSG00000086938	39	26	38	32	46	27
+ENSMUSG00000047938	0	0	3	0	0	0
+ENSMUSG00000086241	199	88	193	237	111	135
+ENSMUSG00000085435	0	0	0	0	0	0
+ENSMUSG00000089914	4	1	0	3	0	1
+ENSMUSG00000050345	29	9	7	4	6	6
+ENSMUSG00000092578	0	0	0	0	0	0
+ENSMUSG00000086454	0	0	0	0	0	0
+ENSMUSG00000086799	2	0	0	1	2	0
+ENSMUSG00000055555	41	0	0	0	0	1
+ENSMUSG00000090202	0	0	0	0	0	0
+ENSMUSG00000072595	0	0	0	0	0	0
+ENSMUSG00000082612	0	0	0	0	0	0
+ENSMUSG00000044906	171	60	63	70	82	83
+ENSMUSG00000052642	0	0	0	0	0	0
+ENSMUSG00000040919	0	0	0	0	0	0
+ENSMUSG00000093551	0	0	0	0	0	0
+ENSMUSG00000041362	173	53	87	108	82	91
+ENSMUSG00000097129	7	4	8	5	10	5
+ENSMUSG00000096986	3	2	5	3	4	1
+ENSMUSG00000087137	0	0	0	0	0	0
+ENSMUSG00000097841	0	0	0	0	0	0
+ENSMUSG00000086607	0	0	0	0	0	0
+ENSMUSG00000014529	0	0	0	0	0	0
+ENSMUSG00000020992	22	6	10	5	11	15
+ENSMUSG00000074136	13	4	9	9	8	10
+ENSMUSG00000031270	3	3	2	3	4	4
+ENSMUSG00000087045	0	0	0	0	0	0
+ENSMUSG00000092183	4	2	3	2	2	3
+ENSMUSG00000085157	0	0	0	0	1	0
+ENSMUSG00000085496	1	0	0	0	0	0
+ENSMUSG00000086263	0	0	0	0	0	0
+ENSMUSG00000090126	10	2	4	4	6	2
+ENSMUSG00000031325	0	0	0	0	0	0
+ENSMUSG00000029564	3	2	6	1	3	1
+ENSMUSG00000074039	0	0	1	0	0	1
+ENSMUSG00000060491	0	0	0	0	0	0
+ENSMUSG00000086947	0	0	0	0	0	0
+ENSMUSG00000050883	303	224	348	108	233	138
+ENSMUSG00000020299	0	0	0	1	0	0
+ENSMUSG00000039545	10	1	5	3	3	0
+ENSMUSG00000059663	0	0	0	0	0	0
+ENSMUSG00000097276	8	7	7	3	8	6
+ENSMUSG00000068173	0	0	0	0	0	0
+ENSMUSG00000045794	0	0	0	0	0	1
+ENSMUSG00000097091	3	0	2	0	4	8
+ENSMUSG00000097502	3	2	2	1	1	5
+ENSMUSG00000087309	0	0	0	0	0	0
+ENSMUSG00000086377	0	4	5	0	0	0
+ENSMUSG00000093528	0	0	0	0	0	0
+ENSMUSG00000037143	0	0	0	0	0	0
+ENSMUSG00000084798	0	0	3	1	0	1
+ENSMUSG00000028642	7	3	6	0	6	0
+ENSMUSG00000048905	10	3	10	8	4	11
+ENSMUSG00000097032	15	4	11	5	6	9
+ENSMUSG00000086569	0	0	0	0	0	0
+ENSMUSG00000087279	0	0	0	0	2	0
+ENSMUSG00000036463	0	0	0	0	0	0
+ENSMUSG00000051758	0	0	0	0	0	0
+ENSMUSG00000085247	0	0	0	0	0	0
+ENSMUSG00000024546	0	0	0	0	0	0
+ENSMUSG00000028314	2	1	0	0	0	0
+ENSMUSG00000086687	0	0	0	0	0	0
+ENSMUSG00000051198	0	0	0	0	0	0
+ENSMUSG00000029138	1	0	0	0	0	0
+ENSMUSG00000086257	0	0	0	0	0	0
+ENSMUSG00000036921	0	0	0	0	0	0
+ENSMUSG00000005131	2	0	1	0	1	1
+ENSMUSG00000046180	0	0	0	0	0	0
+ENSMUSG00000070984	0	0	0	0	0	0
+ENSMUSG00000097632	7	3	3	4	2	0
+ENSMUSG00000086396	0	0	0	0	0	0
+ENSMUSG00000096197	0	0	1	0	0	0
+ENSMUSG00000085522	0	0	0	0	0	0
+ENSMUSG00000096971	68	52	61	81	75	76
+ENSMUSG00000048994	1	0	0	0	0	1
+ENSMUSG00000086244	0	0	0	0	0	0
+ENSMUSG00000097519	4	0	1	0	1	1
+ENSMUSG00000086277	0	0	0	0	0	0
+ENSMUSG00000022518	111	35	48	31	53	60
+ENSMUSG00000026729	45	25	43	17	33	24
+ENSMUSG00000051728	1	0	0	2	0	0
+ENSMUSG00000097387	0	1	0	1	1	2
+ENSMUSG00000053574	7	2	7	4	7	4
+ENSMUSG00000022002	0	0	0	0	0	0
+ENSMUSG00000051788	0	0	0	0	0	0
+ENSMUSG00000084764	0	0	0	0	0	0
+ENSMUSG00000086273	2	0	0	2	2	2
+ENSMUSG00000084834	57	35	38	31	48	29
+ENSMUSG00000073141	0	0	0	0	0	0
+ENSMUSG00000026882	0	0	0	0	0	0
+ENSMUSG00000090220	0	1	0	0	0	2
+ENSMUSG00000085084	0	0	1	0	0	0
+ENSMUSG00000090457	0	0	0	0	0	0
+ENSMUSG00000037358	0	1	2	1	0	2
+ENSMUSG00000021961	0	1	6	0	0	0
+ENSMUSG00000097587	0	0	0	0	0	0
+ENSMUSG00000012042	0	0	0	0	0	0
+ENSMUSG00000040840	33	6	23	8	12	7
+ENSMUSG00000027811	39	20	9	18	13	41
+ENSMUSG00000051074	8	0	3	4	1	1
+ENSMUSG00000070315	287	213	330	223	341	143
+ENSMUSG00000055159	2	0	3	0	1	0
+ENSMUSG00000086954	0	0	0	0	0	0
+ENSMUSG00000029044	0	0	0	0	0	0
+ENSMUSG00000034063	0	0	1	0	0	0
+ENSMUSG00000039138	0	0	0	0	0	0
+ENSMUSG00000097725	1	0	1	0	0	0
+ENSMUSG00000086365	0	0	0	0	0	0
+ENSMUSG00000087233	0	0	0	0	0	0
+ENSMUSG00000060673	0	0	0	0	0	0
+ENSMUSG00000041068	0	0	0	0	0	0
+ENSMUSG00000084995	0	0	0	0	0	0
+ENSMUSG00000073144	40	14	21	17	18	18
+ENSMUSG00000093772	15	12	11	3	7	5
+ENSMUSG00000097329	16	5	5	2	6	6
+ENSMUSG00000013353	2	1	1	0	0	2
+ENSMUSG00000031938	92	102	90	72	101	94
+ENSMUSG00000066571	694	343	429	324	515	465
+ENSMUSG00000073722	0	0	0	0	0	0
+ENSMUSG00000038199	0	0	0	0	0	0
+ENSMUSG00000022179	69	46	96	65	62	35
+ENSMUSG00000056197	0	0	0	0	0	0
+ENSMUSG00000026774	0	0	0	0	0	0
+ENSMUSG00000014837	4	3	2	11	9	9
+ENSMUSG00000086727	0	1	0	0	0	1
+ENSMUSG00000032023	0	0	0	0	0	0
+ENSMUSG00000056617	4	0	2	0	3	3
+ENSMUSG00000047324	0	0	0	0	0	0
+ENSMUSG00000055061	57	23	24	38	38	30
+ENSMUSG00000055643	0	0	0	0	0	0
+ENSMUSG00000078157	0	1	0	0	0	0
+ENSMUSG00000097775	5	2	5	8	6	7
+ENSMUSG00000046367	0	0	0	0	0	0
+ENSMUSG00000074580	6	3	4	2	6	1
+ENSMUSG00000047490	0	0	0	0	0	0
+ENSMUSG00000058670	0	0	0	0	0	0
+ENSMUSG00000075070	0	1	0	0	0	0
+ENSMUSG00000078962	1	0	0	0	0	0
+ENSMUSG00000079324	1	0	1	0	0	1
+ENSMUSG00000062036	0	0	0	0	0	0
+ENSMUSG00000069925	0	0	0	0	0	0
+ENSMUSG00000048038	1	0	0	0	0	0
+ENSMUSG00000079513	0	0	0	0	0	0
+ENSMUSG00000062391	0	0	0	0	0	0
+ENSMUSG00000037270	1535	987	1191	921	1235	1363
+ENSMUSG00000039851	0	0	0	0	0	1
+ENSMUSG00000097216	0	0	0	0	0	0
+ENSMUSG00000090336	0	0	0	0	0	0
+ENSMUSG00000086796	61	74	75	49	87	66
+ENSMUSG00000055357	0	0	0	0	0	0
+ENSMUSG00000055700	0	0	0	0	0	0
+ENSMUSG00000087487	0	0	0	0	0	0
+ENSMUSG00000025961	1	0	2	0	3	3
+ENSMUSG00000045330	0	0	0	0	0	0
+ENSMUSG00000069971	0	0	0	0	0	0
+ENSMUSG00000013668	0	0	0	0	0	0
+ENSMUSG00000067848	0	0	0	0	0	0
+ENSMUSG00000044084	0	0	0	0	0	0
+ENSMUSG00000079460	0	0	0	0	0	0
+ENSMUSG00000085122	1	0	2	0	1	0
+ENSMUSG00000097908	74	144	79	100	101	47
+ENSMUSG00000097852	2	1	4	3	3	2
+ENSMUSG00000086209	0	0	0	0	0	0
+ENSMUSG00000013158	0	1	1	1	2	0
+ENSMUSG00000084234	0	0	0	0	0	0
+ENSMUSG00000097494	4	3	10	1	0	6
+ENSMUSG00000085796	0	0	0	0	0	0
+ENSMUSG00000090585	0	0	0	0	0	0
+ENSMUSG00000086025	0	0	0	0	0	0
+ENSMUSG00000087475	9	7	6	3	9	5
+ENSMUSG00000027229	0	0	0	0	0	0
+ENSMUSG00000086690	1	0	0	0	0	0
+ENSMUSG00000085820	0	0	0	0	0	0
+ENSMUSG00000050526	0	0	0	0	0	0
+ENSMUSG00000073759	0	0	0	0	0	0
+ENSMUSG00000087396	46	21	25	26	24	29
+ENSMUSG00000026224	0	0	0	0	0	0
+ENSMUSG00000049357	2	3	7	4	3	8
+ENSMUSG00000097407	6	2	7	5	2	2
+ENSMUSG00000084848	5	2	3	3	3	2
+ENSMUSG00000053896	0	0	0	0	0	0
+ENSMUSG00000062224	0	0	0	0	0	0
+ENSMUSG00000029586	0	0	0	0	0	0
+ENSMUSG00000090369	108	83	112	75	91	37
+ENSMUSG00000031631	435	262	313	297	409	306
+ENSMUSG00000071749	0	0	0	0	0	0
+ENSMUSG00000079304	0	0	0	0	0	0
+ENSMUSG00000021874	7	0	0	1	0	1
+ENSMUSG00000079048	0	0	0	0	0	0
+ENSMUSG00000073730	0	0	0	0	0	0
+ENSMUSG00000074734	0	0	0	0	0	0
+ENSMUSG00000085198	0	0	0	0	0	0
+ENSMUSG00000071763	0	0	0	0	0	0
+ENSMUSG00000097262	1	0	0	0	0	0
+ENSMUSG00000021415	0	31	22	22	0	0
+ENSMUSG00000097637	40	28	38	30	50	21
+ENSMUSG00000030463	0	0	0	0	0	0
+ENSMUSG00000085037	119	51	74	59	96	96
+ENSMUSG00000070332	32	49	68	42	42	33
+ENSMUSG00000085785	0	0	0	0	0	0
+ENSMUSG00000021718	0	0	0	0	0	0
+ENSMUSG00000086446	0	0	1	0	0	0
+ENSMUSG00000021133	27	11	17	15	22	18
+ENSMUSG00000055403	0	0	0	0	0	0
+ENSMUSG00000020807	193	75	109	79	79	117
+ENSMUSG00000044276	1	1	2	1	1	1
+ENSMUSG00000033015	0	0	0	0	0	0
+ENSMUSG00000030877	2	1	0	1	0	1
+ENSMUSG00000085928	0	0	0	0	0	0
+ENSMUSG00000086355	0	0	0	0	0	0
+ENSMUSG00000058046	2	4	3	2	3	5
+ENSMUSG00000086892	0	0	0	0	0	0
+ENSMUSG00000086968	102	43	78	96	70	142
+ENSMUSG00000036770	1	0	0	0	0	0
+ENSMUSG00000097044	0	0	0	0	0	0
+ENSMUSG00000097021	4	1	0	2	0	2
+ENSMUSG00000027942	311	193	281	250	336	312
+ENSMUSG00000035057	0	0	0	0	0	0
+ENSMUSG00000031736	2	4	4	3	1	0
+ENSMUSG00000025288	0	0	0	0	0	0
+ENSMUSG00000093617	6	1	0	0	5	7
+ENSMUSG00000072893	73	44	47	40	57	46
+ENSMUSG00000085184	4	3	1	0	2	1
+ENSMUSG00000097082	1	0	4	0	3	4
+ENSMUSG00000045928	0	0	0	0	0	0
+ENSMUSG00000051940	0	0	0	0	0	0
+ENSMUSG00000034959	64	16	36	30	13	18
+ENSMUSG00000073147	217	93	166	118	178	192
+ENSMUSG00000085129	9	4	4	11	6	6
+ENSMUSG00000044574	0	0	0	0	0	0
+ENSMUSG00000097885	6	1	2	2	2	0
+ENSMUSG00000036046	1374	858	1055	838	917	1196
+ENSMUSG00000055137	558	652	687	315	846	515
+ENSMUSG00000087455	8	0	2	3	0	1
+ENSMUSG00000086822	0	0	0	0	0	0
+ENSMUSG00000040412	51	14	52	23	18	16
+ENSMUSG00000022639	41	9	13	19	24	18
+ENSMUSG00000087620	0	0	0	0	0	0
+ENSMUSG00000094113	0	0	0	0	0	0
+ENSMUSG00000044121	0	0	0	0	0	0
+ENSMUSG00000085776	1	0	0	0	1	2
+ENSMUSG00000085741	2	3	2	3	1	1
+ENSMUSG00000097772	73	47	49	27	79	45
+ENSMUSG00000028475	20	6	14	8	7	13
+ENSMUSG00000074918	173	111	115	170	185	175
+ENSMUSG00000006204	0	0	0	0	0	0
+ENSMUSG00000067613	0	0	1	1	0	0
+ENSMUSG00000021566	0	0	0	0	0	0
+ENSMUSG00000085004	0	0	0	0	0	0
+ENSMUSG00000025058	87	10	32	22	18	21
+ENSMUSG00000052688	155	30	54	73	33	63
+ENSMUSG00000055594	0	0	0	0	0	0
+ENSMUSG00000020703	0	0	0	0	0	0
+ENSMUSG00000087174	82	44	68	45	60	46
+ENSMUSG00000087424	10	10	11	9	9	14
+ENSMUSG00000073755	2	0	2	1	1	2
+ENSMUSG00000087553	0	0	0	0	0	0
+ENSMUSG00000081793	0	0	1	0	0	0
+ENSMUSG00000097766	0	0	0	0	0	1
+ENSMUSG00000097191	0	0	0	0	0	1
+ENSMUSG00000091370	2	4	1	3	7	2
+ENSMUSG00000057181	540	306	400	355	504	467
+ENSMUSG00000086126	0	0	0	0	0	0
+ENSMUSG00000062046	0	0	0	2	0	0
+ENSMUSG00000093459	40	16	25	12	28	13
+ENSMUSG00000073197	0	0	0	0	0	0
+ENSMUSG00000050549	110	55	68	54	72	95
+ENSMUSG00000073101	6	2	3	3	6	7
+ENSMUSG00000041605	14	3	2	1	2	13
+ENSMUSG00000062470	17	6	16	9	13	13
+ENSMUSG00000045968	4	3	5	3	5	63
+ENSMUSG00000086259	0	0	0	0	2	0
+ENSMUSG00000054672	2	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/per_base_coverage_default.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,299 @@
+#chr	pos	coverage
+test_chromosome	53	1
+test_chromosome	54	1
+test_chromosome	55	2
+test_chromosome	56	3
+test_chromosome	57	3
+test_chromosome	58	4
+test_chromosome	59	4
+test_chromosome	60	4
+test_chromosome	61	5
+test_chromosome	62	5
+test_chromosome	63	5
+test_chromosome	64	5
+test_chromosome	65	5
+test_chromosome	66	5
+test_chromosome	67	5
+test_chromosome	68	5
+test_chromosome	69	5
+test_chromosome	70	5
+test_chromosome	71	5
+test_chromosome	72	6
+test_chromosome	73	6
+test_chromosome	74	6
+test_chromosome	75	6
+test_chromosome	76	6
+test_chromosome	77	6
+test_chromosome	78	8
+test_chromosome	79	8
+test_chromosome	80	8
+test_chromosome	81	8
+test_chromosome	82	8
+test_chromosome	83	9
+test_chromosome	84	9
+test_chromosome	85	9
+test_chromosome	86	10
+test_chromosome	87	10
+test_chromosome	88	11
+test_chromosome	89	12
+test_chromosome	90	12
+test_chromosome	91	13
+test_chromosome	92	14
+test_chromosome	93	14
+test_chromosome	94	16
+test_chromosome	95	16
+test_chromosome	96	17
+test_chromosome	97	17
+test_chromosome	98	18
+test_chromosome	99	18
+test_chromosome	100	18
+test_chromosome	101	21
+test_chromosome	102	22
+test_chromosome	103	23
+test_chromosome	104	23
+test_chromosome	105	23
+test_chromosome	106	24
+test_chromosome	107	25
+test_chromosome	108	25
+test_chromosome	109	25
+test_chromosome	110	25
+test_chromosome	111	25
+test_chromosome	112	25
+test_chromosome	113	25
+test_chromosome	114	25
+test_chromosome	115	26
+test_chromosome	116	26
+test_chromosome	117	26
+test_chromosome	118	26
+test_chromosome	119	26
+test_chromosome	120	26
+test_chromosome	121	26
+test_chromosome	122	27
+test_chromosome	123	29
+test_chromosome	124	29
+test_chromosome	125	32
+test_chromosome	126	32
+test_chromosome	127	33
+test_chromosome	128	33
+test_chromosome	129	33
+test_chromosome	130	32
+test_chromosome	131	32
+test_chromosome	132	33
+test_chromosome	133	32
+test_chromosome	134	32
+test_chromosome	135	34
+test_chromosome	136	33
+test_chromosome	137	33
+test_chromosome	138	33
+test_chromosome	139	34
+test_chromosome	140	34
+test_chromosome	141	35
+test_chromosome	142	37
+test_chromosome	143	37
+test_chromosome	144	38
+test_chromosome	145	38
+test_chromosome	146	38
+test_chromosome	147	38
+test_chromosome	148	38
+test_chromosome	149	38
+test_chromosome	150	38
+test_chromosome	151	38
+test_chromosome	152	38
+test_chromosome	153	36
+test_chromosome	154	36
+test_chromosome	155	37
+test_chromosome	156	37
+test_chromosome	157	37
+test_chromosome	158	36
+test_chromosome	159	36
+test_chromosome	160	37
+test_chromosome	161	36
+test_chromosome	162	37
+test_chromosome	163	36
+test_chromosome	164	35
+test_chromosome	165	37
+test_chromosome	166	36
+test_chromosome	167	36
+test_chromosome	168	36
+test_chromosome	169	34
+test_chromosome	170	36
+test_chromosome	171	36
+test_chromosome	172	36
+test_chromosome	173	35
+test_chromosome	174	35
+test_chromosome	175	36
+test_chromosome	176	33
+test_chromosome	177	32
+test_chromosome	178	32
+test_chromosome	179	32
+test_chromosome	180	32
+test_chromosome	181	32
+test_chromosome	182	31
+test_chromosome	183	31
+test_chromosome	184	32
+test_chromosome	185	32
+test_chromosome	186	32
+test_chromosome	187	32
+test_chromosome	188	32
+test_chromosome	189	32
+test_chromosome	190	31
+test_chromosome	191	31
+test_chromosome	192	31
+test_chromosome	193	31
+test_chromosome	194	32
+test_chromosome	195	32
+test_chromosome	196	32
+test_chromosome	197	32
+test_chromosome	198	30
+test_chromosome	199	29
+test_chromosome	200	28
+test_chromosome	201	31
+test_chromosome	202	30
+test_chromosome	203	29
+test_chromosome	204	30
+test_chromosome	205	31
+test_chromosome	206	31
+test_chromosome	207	31
+test_chromosome	208	32
+test_chromosome	209	31
+test_chromosome	210	31
+test_chromosome	211	31
+test_chromosome	212	31
+test_chromosome	213	31
+test_chromosome	214	31
+test_chromosome	215	31
+test_chromosome	216	30
+test_chromosome	217	28
+test_chromosome	218	28
+test_chromosome	219	27
+test_chromosome	220	27
+test_chromosome	221	28
+test_chromosome	222	28
+test_chromosome	223	28
+test_chromosome	224	28
+test_chromosome	225	29
+test_chromosome	226	29
+test_chromosome	227	30
+test_chromosome	228	30
+test_chromosome	229	31
+test_chromosome	230	30
+test_chromosome	231	31
+test_chromosome	232	32
+test_chromosome	233	33
+test_chromosome	234	34
+test_chromosome	235	33
+test_chromosome	236	33
+test_chromosome	237	32
+test_chromosome	238	32
+test_chromosome	239	32
+test_chromosome	240	30
+test_chromosome	241	30
+test_chromosome	242	29
+test_chromosome	243	31
+test_chromosome	244	32
+test_chromosome	245	30
+test_chromosome	246	29
+test_chromosome	247	29
+test_chromosome	248	29
+test_chromosome	249	29
+test_chromosome	250	28
+test_chromosome	351	31
+test_chromosome	352	32
+test_chromosome	353	33
+test_chromosome	354	34
+test_chromosome	355	35
+test_chromosome	356	34
+test_chromosome	357	34
+test_chromosome	358	35
+test_chromosome	359	34
+test_chromosome	360	35
+test_chromosome	361	35
+test_chromosome	362	36
+test_chromosome	363	36
+test_chromosome	364	36
+test_chromosome	365	36
+test_chromosome	366	37
+test_chromosome	367	37
+test_chromosome	368	37
+test_chromosome	369	37
+test_chromosome	370	36
+test_chromosome	371	37
+test_chromosome	372	37
+test_chromosome	373	39
+test_chromosome	374	39
+test_chromosome	375	38
+test_chromosome	376	36
+test_chromosome	377	36
+test_chromosome	378	36
+test_chromosome	379	36
+test_chromosome	380	34
+test_chromosome	381	33
+test_chromosome	382	32
+test_chromosome	383	32
+test_chromosome	384	31
+test_chromosome	385	31
+test_chromosome	386	31
+test_chromosome	387	31
+test_chromosome	388	31
+test_chromosome	389	30
+test_chromosome	390	30
+test_chromosome	391	30
+test_chromosome	392	30
+test_chromosome	393	30
+test_chromosome	394	30
+test_chromosome	395	30
+test_chromosome	396	29
+test_chromosome	397	28
+test_chromosome	398	28
+test_chromosome	399	28
+test_chromosome	400	27
+test_chromosome	501	25
+test_chromosome	502	25
+test_chromosome	503	25
+test_chromosome	504	25
+test_chromosome	505	25
+test_chromosome	506	24
+test_chromosome	507	23
+test_chromosome	508	22
+test_chromosome	509	21
+test_chromosome	510	21
+test_chromosome	511	21
+test_chromosome	512	21
+test_chromosome	513	21
+test_chromosome	514	21
+test_chromosome	515	21
+test_chromosome	516	21
+test_chromosome	517	20
+test_chromosome	518	18
+test_chromosome	519	17
+test_chromosome	520	17
+test_chromosome	521	17
+test_chromosome	522	16
+test_chromosome	523	15
+test_chromosome	524	15
+test_chromosome	525	14
+test_chromosome	526	14
+test_chromosome	527	13
+test_chromosome	528	12
+test_chromosome	529	11
+test_chromosome	530	10
+test_chromosome	531	10
+test_chromosome	532	10
+test_chromosome	533	9
+test_chromosome	534	9
+test_chromosome	535	8
+test_chromosome	536	8
+test_chromosome	537	7
+test_chromosome	538	7
+test_chromosome	539	7
+test_chromosome	540	7
+test_chromosome	541	6
+test_chromosome	542	6
+test_chromosome	543	6
+test_chromosome	544	5
+test_chromosome	545	5
+test_chromosome	546	4
+test_chromosome	547	4
+test_chromosome	548	2
+test_chromosome	549	2
+test_chromosome	550	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/per_base_coverage_inside_features.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,199 @@
+#chr	pos	coverage
+test_chromosome	53	1
+test_chromosome	54	1
+test_chromosome	55	2
+test_chromosome	56	3
+test_chromosome	57	3
+test_chromosome	58	4
+test_chromosome	59	4
+test_chromosome	60	4
+test_chromosome	61	5
+test_chromosome	62	5
+test_chromosome	63	5
+test_chromosome	64	5
+test_chromosome	65	5
+test_chromosome	66	5
+test_chromosome	67	5
+test_chromosome	68	5
+test_chromosome	69	5
+test_chromosome	70	5
+test_chromosome	71	5
+test_chromosome	72	6
+test_chromosome	73	6
+test_chromosome	74	6
+test_chromosome	75	6
+test_chromosome	76	6
+test_chromosome	77	6
+test_chromosome	78	8
+test_chromosome	79	8
+test_chromosome	80	8
+test_chromosome	81	8
+test_chromosome	82	8
+test_chromosome	83	9
+test_chromosome	84	9
+test_chromosome	85	9
+test_chromosome	86	10
+test_chromosome	87	10
+test_chromosome	88	11
+test_chromosome	89	12
+test_chromosome	90	12
+test_chromosome	91	13
+test_chromosome	92	14
+test_chromosome	93	14
+test_chromosome	94	16
+test_chromosome	95	16
+test_chromosome	96	17
+test_chromosome	97	17
+test_chromosome	98	18
+test_chromosome	99	18
+test_chromosome	100	18
+test_chromosome	101	21
+test_chromosome	102	22
+test_chromosome	103	23
+test_chromosome	104	23
+test_chromosome	105	23
+test_chromosome	106	24
+test_chromosome	107	25
+test_chromosome	108	25
+test_chromosome	109	25
+test_chromosome	110	25
+test_chromosome	111	25
+test_chromosome	112	25
+test_chromosome	113	25
+test_chromosome	114	25
+test_chromosome	115	26
+test_chromosome	116	26
+test_chromosome	117	26
+test_chromosome	118	26
+test_chromosome	119	26
+test_chromosome	120	26
+test_chromosome	121	26
+test_chromosome	122	27
+test_chromosome	123	29
+test_chromosome	124	29
+test_chromosome	125	32
+test_chromosome	126	32
+test_chromosome	127	33
+test_chromosome	128	33
+test_chromosome	129	33
+test_chromosome	130	32
+test_chromosome	131	32
+test_chromosome	132	33
+test_chromosome	133	32
+test_chromosome	134	32
+test_chromosome	135	34
+test_chromosome	136	33
+test_chromosome	137	33
+test_chromosome	138	33
+test_chromosome	139	34
+test_chromosome	140	34
+test_chromosome	141	35
+test_chromosome	142	37
+test_chromosome	143	37
+test_chromosome	144	38
+test_chromosome	145	38
+test_chromosome	146	38
+test_chromosome	147	38
+test_chromosome	148	38
+test_chromosome	149	38
+test_chromosome	150	38
+test_chromosome	151	38
+test_chromosome	152	38
+test_chromosome	153	36
+test_chromosome	154	36
+test_chromosome	155	37
+test_chromosome	156	37
+test_chromosome	157	37
+test_chromosome	158	36
+test_chromosome	159	36
+test_chromosome	160	37
+test_chromosome	161	36
+test_chromosome	162	37
+test_chromosome	163	36
+test_chromosome	164	35
+test_chromosome	165	37
+test_chromosome	166	36
+test_chromosome	167	36
+test_chromosome	168	36
+test_chromosome	169	34
+test_chromosome	170	36
+test_chromosome	171	36
+test_chromosome	172	36
+test_chromosome	173	35
+test_chromosome	174	35
+test_chromosome	175	36
+test_chromosome	176	33
+test_chromosome	177	32
+test_chromosome	178	32
+test_chromosome	179	32
+test_chromosome	180	32
+test_chromosome	181	32
+test_chromosome	182	31
+test_chromosome	183	31
+test_chromosome	184	32
+test_chromosome	185	32
+test_chromosome	186	32
+test_chromosome	187	32
+test_chromosome	188	32
+test_chromosome	189	32
+test_chromosome	190	31
+test_chromosome	191	31
+test_chromosome	192	31
+test_chromosome	193	31
+test_chromosome	194	32
+test_chromosome	195	32
+test_chromosome	196	32
+test_chromosome	197	32
+test_chromosome	198	30
+test_chromosome	199	29
+test_chromosome	200	28
+test_chromosome	201	31
+test_chromosome	202	30
+test_chromosome	203	29
+test_chromosome	204	30
+test_chromosome	205	31
+test_chromosome	206	31
+test_chromosome	207	31
+test_chromosome	208	32
+test_chromosome	209	31
+test_chromosome	210	31
+test_chromosome	211	31
+test_chromosome	212	31
+test_chromosome	213	31
+test_chromosome	214	31
+test_chromosome	215	31
+test_chromosome	216	30
+test_chromosome	217	28
+test_chromosome	218	28
+test_chromosome	219	27
+test_chromosome	220	27
+test_chromosome	221	28
+test_chromosome	222	28
+test_chromosome	223	28
+test_chromosome	224	28
+test_chromosome	225	29
+test_chromosome	226	29
+test_chromosome	227	30
+test_chromosome	228	30
+test_chromosome	229	31
+test_chromosome	230	30
+test_chromosome	231	31
+test_chromosome	232	32
+test_chromosome	233	33
+test_chromosome	234	34
+test_chromosome	235	33
+test_chromosome	236	33
+test_chromosome	237	32
+test_chromosome	238	32
+test_chromosome	239	32
+test_chromosome	240	30
+test_chromosome	241	30
+test_chromosome	242	29
+test_chromosome	243	31
+test_chromosome	244	32
+test_chromosome	245	30
+test_chromosome	246	29
+test_chromosome	247	29
+test_chromosome	248	29
+test_chromosome	249	29
+test_chromosome	250	28
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/per_base_coverage_outside_features.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,101 @@
+#chr	pos	coverage
+test_chromosome	351	31
+test_chromosome	352	32
+test_chromosome	353	33
+test_chromosome	354	34
+test_chromosome	355	35
+test_chromosome	356	34
+test_chromosome	357	34
+test_chromosome	358	35
+test_chromosome	359	34
+test_chromosome	360	35
+test_chromosome	361	35
+test_chromosome	362	36
+test_chromosome	363	36
+test_chromosome	364	36
+test_chromosome	365	36
+test_chromosome	366	37
+test_chromosome	367	37
+test_chromosome	368	37
+test_chromosome	369	37
+test_chromosome	370	36
+test_chromosome	371	37
+test_chromosome	372	37
+test_chromosome	373	39
+test_chromosome	374	39
+test_chromosome	375	38
+test_chromosome	376	36
+test_chromosome	377	36
+test_chromosome	378	36
+test_chromosome	379	36
+test_chromosome	380	34
+test_chromosome	381	33
+test_chromosome	382	32
+test_chromosome	383	32
+test_chromosome	384	31
+test_chromosome	385	31
+test_chromosome	386	31
+test_chromosome	387	31
+test_chromosome	388	31
+test_chromosome	389	30
+test_chromosome	390	30
+test_chromosome	391	30
+test_chromosome	392	30
+test_chromosome	393	30
+test_chromosome	394	30
+test_chromosome	395	30
+test_chromosome	396	29
+test_chromosome	397	28
+test_chromosome	398	28
+test_chromosome	399	28
+test_chromosome	400	27
+test_chromosome	501	25
+test_chromosome	502	25
+test_chromosome	503	25
+test_chromosome	504	25
+test_chromosome	505	25
+test_chromosome	506	24
+test_chromosome	507	23
+test_chromosome	508	22
+test_chromosome	509	21
+test_chromosome	510	21
+test_chromosome	511	21
+test_chromosome	512	21
+test_chromosome	513	21
+test_chromosome	514	21
+test_chromosome	515	21
+test_chromosome	516	21
+test_chromosome	517	20
+test_chromosome	518	18
+test_chromosome	519	17
+test_chromosome	520	17
+test_chromosome	521	17
+test_chromosome	522	16
+test_chromosome	523	15
+test_chromosome	524	15
+test_chromosome	525	14
+test_chromosome	526	14
+test_chromosome	527	13
+test_chromosome	528	12
+test_chromosome	529	11
+test_chromosome	530	10
+test_chromosome	531	10
+test_chromosome	532	10
+test_chromosome	533	9
+test_chromosome	534	9
+test_chromosome	535	8
+test_chromosome	536	8
+test_chromosome	537	7
+test_chromosome	538	7
+test_chromosome	539	7
+test_chromosome	540	7
+test_chromosome	541	6
+test_chromosome	542	6
+test_chromosome	543	6
+test_chromosome	544	5
+test_chromosome	545	5
+test_chromosome	546	4
+test_chromosome	547	4
+test_chromosome	548	2
+test_chromosome	549	2
+test_chromosome	550	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaseq_qc_counts_custom.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,2 @@
+#GeneID	try_this
+GENE1	45
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaseq_qc_results_custom.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,48 @@
+RNA-Seq QC report
+-----------------------------------
+
+>>>>>>> Input
+
+    bam file = /tmp/tmp_CFvEQ/files/000/dataset_49.dat
+    gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat
+    counting algorithm = proportional
+    protocol = strand-specific-forward
+
+
+>>>>>>> Reads alignment
+
+    reads aligned (left/right) = 0 / 0
+    read pairs aligned  = 0
+    total alignments = 101
+    secondary alignments = 1
+    non-unique alignments = 0
+    aligned to genes  = 46
+    ambiguous alignments = 0
+    no feature assigned = 55
+    not aligned = 0
+
+
+>>>>>>> Reads genomic origin
+
+    exonic =  46 (45.54%)
+    intronic = 0 (0%)
+    intergenic = 55 (54.46%)
+    overlapping exon = 0 (0%)
+
+
+>>>>>>> Transcript coverage profile
+
+    5' bias = NaN
+    3' bias = NaN
+    5'-3' bias = NaN
+
+
+>>>>>>> Junction analysis
+
+    reads at junctions = 53
+
+    CTTT : 47.17%
+    CCAC : 47.17%
+    GCAC : 1.89%
+    CTAC : 1.89%
+    GAAT : 1.89%
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rnaseq_qc_results_default.txt	Thu Oct 10 17:40:46 2019 -0400
@@ -0,0 +1,47 @@
+RNA-Seq QC report
+-----------------------------------
+
+>>>>>>> Input
+
+    bam file = /tmp/tmp_CFvEQ/files/000/dataset_1.dat
+    gff file = /tmp/tmp_CFvEQ/files/000/dataset_2.dat
+    counting algorithm = uniquely-mapped-reads
+    protocol = non-strand-specific
+
+
+>>>>>>> Reads alignment
+
+    reads aligned  = 100
+    total alignments = 101
+    secondary alignments = 1
+    non-unique alignments = 2
+    aligned to genes  = 54
+    ambiguous alignments = 0
+    no feature assigned = 45
+    not aligned = 0
+    SSP estimation (fwd/rev) = 0.59 / 0.41
+
+
+>>>>>>> Reads genomic origin
+
+    exonic =  54 (54.55%)
+    intronic = 0 (0%)
+    intergenic = 45 (45.45%)
+    overlapping exon = 0 (0%)
+
+
+>>>>>>> Transcript coverage profile
+
+    5' bias = NaN
+    3' bias = NaN
+    5'-3' bias = NaN
+
+
+>>>>>>> Junction analysis
+
+    reads at junctions = 52
+
+    CTTT : 48.08%
+    CCAC : 48.08%
+    GCAC : 1.92%
+    CTAC : 1.92%
Binary file test-data/test_mapped_reads.bam has changed