Table 1

Details of the 12 samples established as a proficiency testing panel for this study showing sequencing data generated during the deployed phase at sea which was reanalysed using the Epi2Me toolkit and the ARTIC pipeline

Sample IDLineageClade (variant)ReadsCoverageQuality scoreCt valueOriginal variant assignedCOG variant reported
Sample 1_Barcode 13None21J (Delta)18 94465%Poor16.72DeltaDelta
Sample 2_ Barcode 14None21J (Delta)12 79172%Poor16.64DeltaDelta
Sample 3_ Barcode 15AY.421J (Delta)45 909>99%Good20DeltaDelta
Sample 4_ Barcode 16AY.12621J (Delta)88 382>99%Good22.45DeltaDelta
Sample 5_ Barcode 17AY.421J (Delta)50 075>99%Good25.08DeltaDelta
Sample 6_ Barcode 18AY.4321J (Delta)49 58898%Good19.63DeltaDelta
Sample 7_ Barcode 19AY.4621J (Delta)110 459>99%Good23.94DeltaDelta
Sample 8_ Barcode 20AY.421J (Delta)109 764>99%Good24.1DeltaDelta
Sample 9_ Barcode 21AY.421J (Delta)41 15297%Good19.08DeltaDelta
Sample 10_ Barcode 22BA.121K (Omicron)153 822>99%Good26.28OmicronOmicron
Sample 11_ Barcode 23BA.121K (Omicron)74 939>99%Good29.96OmicronOmicron
  • The original variant assignment performed using the CLC Genomics Workbench at sea is shown in the final column (COG variant reported). Quality scores were calculated as part of the ARTIC workflow analysis in Epi2Me.

  • COG, COVID-19 Genomics Consortium; N/A, not applicable; NTC, non-template control.