+
+
+ Sample Info
+
+
+ i
+
+ High-level data and metadata about this sample.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {{ sample.info[0] }}
+
+
+ {{ sample.info[1] }}
+
+
+ {{ sample.info[2] }}
+
+
+ {{ sample.info[3] }}
+
+
+ Year
+ Date of Collection
+ Date of Sequencing
+ Species +
+ + Date of Collection
+ Date of Sequencing
+ Species +
+
+
+
+
+
+
+
+
+
+
+ Location Info
+
+
+
+ i
+
+ Information about where the sample was collected.
+
+
+
+
+ Country
+
+
+ Latitude
+
+
+ Longitude
+
+
+ Health Facility
+
+ Region
+
+ District
+
+ Type
+
+
+ {{ sample.location_info[2] }}
+
+
+ {{ sample.location_info[0] }}
+
+
+ {{ sample.location_info[1] }}
+
+
+ {{ sample.location_info[3] }}
+
+
+ {{ sample.location_info[4] }}
+
+
+ {{ sample.location_info[5] }}
+
+
+ {{ sample.location_info[6] }}
+
+
+
+ Predicted RDT Region Presence
+
+
+
+ i
+
+ The presence of the HRP-2 and HRP-3 regions is presented below. "+" indicates the presence of either region ; "-" indicates the absence of the region.
+
+ Presence or absence is determined by examining the coverage for this sample. If the coverage over a region is less than 5% of the coverage of the containing contig, that region is said to be deleted (for HRP-2: Pf3D7_08_V3:1373212-1376988; for HRP-3: Pf3D7_13_v3:2840236-2842840). Otherwise the region is counted as present. + +
+ + Presence or absence is determined by examining the coverage for this sample. If the coverage over a region is less than 5% of the coverage of the containing contig, that region is said to be deleted (for HRP-2: Pf3D7_08_V3:1373212-1376988; for HRP-3: Pf3D7_13_v3:2840236-2842840). Otherwise the region is counted as present. + +
+
+
+
+
+ {{ sample.hrp2 }}
HRP-2 Result
+
+ {{ sample.hrp3 }}
HRP-3 Result
+
+
+
+
+ Map
+
+ i
+
+ Interactive map showing where the sample was collected.
+
+
+
+ {{ sample.map|safe }}
+
+
+
+
+
+ Predicted Drug Sensitivities
+
+
+ i
+
+ Sensitivity and resistance to widely used anti-malarial drugs are shown in the table.
+
+ Presence of individual markers (i.e. variants / mutation events / protein changes) are shown in the plot. Red markers indicate the presence of a potential drug-resistance-related mutation event in this sample. White markers indicate the absence of such a marker. Amino acid changes are indicated by vertical labels, grouped by gene (column group labels). +
+ The drug resistance markers shown below are defined in the methods the PF7 callset from the Sanger Institute. Each listed drug has a rubric by which resistance or sensitivity is determined based on the presence or absence of specific genotypes at known protein change sites. +
+ For more information, see: + Pf7 Resistance Classification + +
+ + Presence of individual markers (i.e. variants / mutation events / protein changes) are shown in the plot. Red markers indicate the presence of a potential drug-resistance-related mutation event in this sample. White markers indicate the absence of such a marker. Amino acid changes are indicated by vertical labels, grouped by gene (column group labels). +
+ The drug resistance markers shown below are defined in the methods the PF7 callset from the Sanger Institute. Each listed drug has a rubric by which resistance or sensitivity is determined based on the presence or absence of specific genotypes at known protein change sites. +
+ For more information, see: + Pf7 Resistance Classification + +
+
+
+
+
+
+
+
+
+ | + | Chloroquine | +Pyrimethamine | +Sulfadoxine | +Mefloquine | +Artemisinin | +Piperaquine | +
|---|---|---|---|---|---|---|
| Sensitivity | + {% for item in sample.drug_res %} + {% if item == "RESISTANT" %} +{{ item }} | + {% elif item == "SENSITIVE" %} +{{ item }} | + {% else %} +{{ item }} | + {% endif %} + {% endfor %} +
+ .decode('utf-8') | safe }})
+
+
+
+
+
+ Marker Absent
+
+
+ Marker Present
+
+
+
+
+
+
+
+ QC Info
+
+
+ i
+
+ Metrics about the quality of this sample.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ {{ sample.info[4] }}
+
+
+ {{ sample.info[5]|int }}
+
+
+
+ {% if sample.info[6] != "N/A" %}
+ {{ sample.info[6] }}%
+ {% else %}
+ {{ sample.info[6] }}
+ {% endif %}
+
+
+ {{ sample.info[8] }}
+
+
+ Aligned Fold Coverage
+ Aligned Read Length
+ Percent Properly Paired Reads
+ Read Quality Mean +
+ + Aligned Read Length
+ Percent Properly Paired Reads
+ Read Quality Mean +
.decode('utf-8') | safe }})
.decode('utf-8') | safe }})
+ .decode('utf-8') | safe }})
+