GPSEA cohort analysis

Successfully loaded {{ n_individuals }} individuals. {{ n_male }} were recorded as male, {{ n_female }} as female, and {{ n_unknown_sex }} as unknown sex. {{ n_alive }} were reported to be alive at the time of last encounter, and {{ n_deceased }} were deceased. {{ n_has_disease_onset }} had disease onset information and {{n_has_age_at_last_encounter }} had information about the age at last encounter. In the cohort, there were a total of {{ total_hpo_count }} HPO terms used for annotation. {% if total_measurement_count > 0 %} Information was provided for {{ total_measurement_count }} measurement assays. {% endif %}

{% if n_excluded > 0 %}

Not able to load {{ n_excluded }} individuals.

{% else %}

No errors encountered.

{% endif %} {% for hpo_count in hpo_counts %} {% endfor %}

Top {{top_hpo_count}} HPO Terms

A total of {{ total_hpo_count }} HPO terms were used to annotated the cohort.
HPO Term ID Seen in n individuals
{{ hpo_count.HPO }} {{ hpo_count.ID }} {{ hpo_count.Count }}
{% if n_has_onset_info > 0 %}

{{ n_has_onset_info }} had onset information for at least 20% of individuals.

Top {{top_var_count}} HPO Terms

A total of {{ total_hpo_count }} HPO terms were used to annotated the cohort. HPO Count {% for onset_info in has_onset_information %} {{ onset_info.display_label }} {{ onset_info.count }} {% endfor %} {% endif %}
{% for var_count in var_counts %} {% endfor %}

Top {{top_var_count}} Variants

Variants are shown according to {{ transcript_id }}. A total of {{ unique_variant_count}} unique variants were identified in the cohort.
Seen in n individuals Variant key Variant Name Protein Variant Variant Class
{{ var_count.Count }} {{ var_count.variant }} {{ var_count.variant_name }} {{ var_count.protein_name }} {{ var_count.variant_effects }}
{% for disease_count in disease_counts %} {% endfor %}

Diseases

Disease Name Disease ID Annotation Count
{{ disease_count.disease_name }} {{ disease_count.disease_id }} {{ disease_count.count }}
{% if has_transcript > 0 %} {% for var_effect in var_effects_list %} {% endfor %}

Variant categories for {{ transcript_id }}

Variant effect Annotation Count Percent
{{ var_effect.effect }} {{ var_effect.count }} {{ var_effect.percent }}
{% else %}

Call this function with transcript to see table with variant effect counts.

{% endif %}