Rapport genererad: {{ date }}
+ + +| + Ticket ID (CG Projekt ID) + | {{ topsample.projects.Customer_ID_project }} ({{ topsample.projects.CG_ID_project }}) | +|
| + Kund ID (*) + | {{ topsample.projects.Customer_ID }} | +|
| Rapport version | + {% if reports|length > 1 %} +Version {{ reports[0].version }}, {{ reports[0].date.date() }} (Ersätter version {{ reports[1].version }}, {{ reports[1].date.date() }}) | + {% else %} +Version {{ reports[0].version }}, {{ reports[0].date.date() }} | + {% endif %} +
| Ansvarig bioinformatiker | +{{ user }} | +|
| microSALT version | +{{ build }} | +
| Prov ID (*) | +CG Prov ID | +Applikationstag | +Organism (*) | +Referensgenom (*) | +Antal Reads (**) | +Mappningsgrad % | +Duplikationsgrad % | +Insert Storlek (Median) | +Medeltäckning | +%BP > 10x Täckning | +%BP > 30x Täckning | +%BP > 50x Täckning | +%BP > 100x Täckning | +|||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| {{ sample.Customer_ID_sample }} | +{{ sample.CG_ID_sample }} | + {% if sample.application_tag and sample.application_tag[-1:]|float != 0 %} +{{ sample.application_tag }} | + {% else %} +{{ sample.application_tag }} | + {% endif %} + {% if sample.organism is not none %} +{{ sample.organism.replace('_', ' ').capitalize() }} | + {% else %}Okänd | {% endif %} +{{ sample.reference_genome }} | + {% if sample.total_reads is none %} ++ 0 + {% else %} + {% if sample.application_tag and sample.application_tag[-1:]|float != 0 %} + {% set bp_perc = ((sample.total_reads*100/((sample.application_tag[-1:]|float)*2000000))|round(2)) %} + {% else %} + {% set bp_perc = 0.0 %} + {% endif %} + {% if 'Kontroll' in sample.ST_status %} + {% if bp_perc > threshold.NTC_total_reads_fail %} + | + {{ '{0:,}'.format(sample.total_reads) |replace(","," ")}} ({{ bp_perc }}%) + {% elif bp_perc > threshold.NTC_total_reads_warn %} + | + {{ '{0:,}'.format(sample.total_reads) |replace(","," ")}} ({{ bp_perc }}%) + {% else %} + | + {{ '{0:,}'.format(sample.total_reads) |replace(","," ")}} ({{ bp_perc }}%) + {% endif %} + {% else %} + {% if bp_perc < threshold.total_reads_fail %} + | + {{ '{0:,}'.format(sample.total_reads) |replace(","," ")}} ({{ bp_perc }}%) + {% elif bp_perc < threshold.total_reads_warn %} + | + {{ '{0:,}'.format(sample.total_reads) |replace(","," ")}} ({{ bp_perc }}%) + {% else %} + | + {{ '{0:,}'.format(sample.total_reads) |replace(","," ")}} ({{ bp_perc }}%) + {% endif %} + {% endif %} + {% endif %} + | + {% if sample.mapped_rate is none or sample.mapped_rate == 0 %} ++ 0.0 + {% elif (sample.mapped_rate*100)|round(2) <= threshold.mapped_rate_warn and not 'Kontroll' in sample.ST_status %} + {% if (sample.mapped_rate*100)|round(2) <= threshold.mapped_rate_fail %} + | + {{ (sample.mapped_rate*100)|round(2) }} + {% else %} + | + {{ (sample.mapped_rate*100)|round(2) }} + {% endif %} + {% else %} | {{ (sample.mapped_rate*100)|round(2) }} {% endif %} | + {% if sample.duplication_rate is none or sample.duplication_rate == -1 or sample.duplication_rate == 0.0 %} ++ N/A + {% elif (sample.duplication_rate*100)|round(2) >= threshold.duplication_rate_warn and not 'Kontroll' in sample.ST_status %} + {% if (sample.duplication_rate*100)|round(2) >= threshold.duplication_rate_fail %} + | + {{ (sample.duplication_rate*100)|round(2) }} + {% else %} + | + {{ (sample.duplication_rate*100)|round(2) }} + {% endif %} + {% else %} + | + {{ (sample.duplication_rate*100)|round(2) }} + {% endif %} + | + {% if sample.insert_size is none or sample.insert_size == 0 %} ++ N/A + {% elif sample.insert_size <= threshold.insert_size_warn and not 'Kontroll' in sample.ST_status %} + {% if sample.insert_size <= threshold.insert_size_fail %} + | + {{ sample.insert_size }} + {% else %} + | + {{ sample.insert_size }} + {% endif %} + {% else %} | {{ sample.insert_size }} {% endif %} | + {% if sample.average_coverage is none or sample.average_coverage|round(2) == 0 %} ++ 0.0x + {% elif (sample.average_coverage)|round(2) <= threshold.average_coverage_warn and not 'Kontroll' in sample.ST_status %} + {% if (sample.average_coverage)|round(2) <= threshold.average_coverage_fail %} + | + {{ (sample.average_coverage)|round(2) }}x + {% else %} + | + {{ (sample.average_coverage)|round(2) }}x + {% endif %} + {% else %} | {{ (sample.average_coverage)|round(2) }}x{% endif %} | + {% if sample.coverage_10x is none or (sample.coverage_10x*100)|round(2) == 0 %} ++ 0.0 + {% elif (sample.coverage_10x*100)|round(2) <= threshold.bp_10x_warn and not 'Kontroll' in sample.ST_status %} + {% if (sample.coverage_10x*100)|round(2) <= threshold.bp_10x_fail %} + | + {{ (sample.coverage_10x*100)|round(2) }} + {% else %} + | + {{ (sample.coverage_10x*100)|round(2) }} + {% endif %} + {% else %} | {{ (sample.coverage_10x*100)|round(2) }} {% endif %} | + {% if sample.coverage_30x is none or (sample.coverage_30x*100)|round(2) == 0 %} ++ 0.0 + {% elif (sample.coverage_30x*100)|round(2) <= threshold.bp_30x_warn and not 'Kontroll' in sample.ST_status %} + | + {{ (sample.coverage_30x*100)|round(2) }} + {% else %} | {{ (sample.coverage_30x*100)|round(2) }} {% endif %} | + {% if sample.coverage_50x is none or (sample.coverage_50x*100)|round(2) == 0 %} ++ 0.0 + {% elif (sample.coverage_50x*100)|round(2) <= threshold.bp_50x_warn and not 'Kontroll' in sample.ST_status %} + | + {{ (sample.coverage_50x*100)|round(2) }} + {% else %} | {{ (sample.coverage_50x*100)|round(2) }} {% endif %} | + {% if sample.coverage_100x is none or (sample.coverage_100x*100)|round(2) == 0 %} ++ 0.0 + {% elif (sample.coverage_100x*100)|round(2) <= threshold.bp_100x_warn and not 'Kontroll' in sample.ST_status %} + | + {{ (sample.coverage_100x*100)|round(2) }} + {% else %} | {{ (sample.coverage_100x*100)|round(2) }} {% endif %} | +
| Prov ID (*) | +Applikationstag (*) | +Organism (*) | +Ankomstdatum | +Datum prep | +Metod prep | +Datum sekvensering | +Metod sekvensering | +Prioritet (*) | +|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| {{ sample.Customer_ID_sample }} | +{{ sample.application_tag }} | + {% if sample.organism is not none %} +{{ sample.organism.replace('_', ' ').capitalize() }} | + {% else %} +N/A | + {% endif %} + {% if sample.date_arrival is not none and sample.date_arrival.date().strftime('%Y-%m-%d') != '1-01-01' %} +{{ sample.date_arrival.date() }} | + {% else %}Okänt | {% endif %} + {% if sample.date_libprep is not none and sample.date_libprep.date().strftime('%Y-%m-%d') != '1-01-01' %} +{{ sample.date_libprep.date() }} | + {% else %}Okänt | {% endif %} + {% if sample.method_libprep is not none and 'Not in LIMS' not in sample.method_libprep %} +{{ sample.method_libprep }} | + {% else %} +Okänt | + {% endif %} + {% if sample.date_sequencing is not none and sample.date_sequencing.date().strftime('%Y-%m-%d') != '1-01-01' %} +{{ sample.date_sequencing.date() }} | + {% else %}Okänt | {% endif %} + {% if sample.method_sequencing is not none and 'Not in LIMS' not in sample.method_sequencing %} +{{ sample.method_sequencing }} | + {% else %} +Okänt | + {% endif %} + {% if sample.priority is not none %} +{{ sample.priority.capitalize() }} | + {% else %} +- | + {% endif %} +
+ {% if topsample.application_tag == "MWRNXTR003" %} + Mikrobiell helgenomssekvensering av rutinprov, med krav på minst 3 miljoner läspar. + Nextera library preparation. + {% elif topsample.application_tag in ["MWGNXTR003", "MWMNXTR003", "MWLNXTR003"] %} + Mikrobiell helgenomssekvensering, med krav på minst 3 miljoner läspar. + Nextera library preparation. + {% elif topsample.application_tag == "MWXNXTR003" %} + Storskalig mikrobiell helgenomssekvensering av minst 176 prover, med krav på minst 3 miljoner läspar. + Nextera library preparation. + {% elif topsample.application_tag in ["VWGNXTR001", "VWLNXTR001"] %} + Virologisk helgenomssekvensering, med krav på minst 1 miljon läspar. + Nextera library preparation. + {% elif topsample.application_tag == "VWSMCTR001" %} + Virologisk helgenomssekvensering, med krav på minst 1 miljon läspar. + MiniCovid kit tagmentation preparation. + {% elif topsample.application_tag == "MWSMCTR003" %} + Mikrobiell helgenomssekvensering, med krav på minst 3 miljoner läspar. + MiniCovid kit tagmentation preparation. + {% endif %} +
++ Tillförlitligheten hos resultaten förutsätter att informationen som bifogats från kund är korrekt. +
+
+ Alla typer av förbättringsförslag mailas med fördel till microsalt-suggestions@scilifelab.se
+
+ Din återkopplling uppskattas!
+
+ All kommunikation gällande ordern såsom tillägg, avvikelser eller + eventuella undantag i metoden från Clinical Genomics finns tillgängligt i + Freshdesk för dess ticket id. En stängd ticket kan närsomhelst + öppnas upp igen för frågor. +
+
+ Valtteri Wirta
+
+ Head of unit, Clinical Genomics
+