{% extends "base.html" %} {% block content %}

Sequencing depth and genome coverage report
Chromosome: {{chrom_name}} {% if project %} Project : {{project_name}} {% endif %}

Coverage

The following figure shows the per-base coverage along the reference genome (black line). The blue line indicates the running median. From the normalised coverage, we estimate z-scores on a per-base level. The red lines indicates the z-scores at plus or minus N standard deviations, where N is chosen by the user (default:4).
The image above is a static image. However, interactive plots are available from the table here below. To allows interactions, we split the data into chunks of 500,000 bp length at max. The names contains the start and end positions. {{ list_submapping }}
The following figure contains the histogram of the genome coverage. The X and Y axis being in log scale.

Basic stats

The following table gives some basic statistics about the genome coverage. {{ nc_stats }}

Regions of Interest

Running median is the median computed along the genome using a sliding window. The following tables give regions of interest detected by sequana. Here is some captions:

Low coverage region

{{ lc_paragraph }} {{ low_coverage }}

High coverage region

{{ hc_paragraph }} {{ high_coverage }}
{% if coverage_vs_gc %}

Coverage versus GC

{{ coverage_vs_gc }}
{% endif %}

Normalized coverage

{{ nc_paragraph }}

Z-Score distribution

{{ bp_paragraph }}
{% endblock %}