Additional file 2 of HPV genotyping by L1 amplicon sequencing of archived invasive cervical cancer samples: a pilot study

Additional file 2. Detailed data for each sample, including archive type, tissue type, histological subtype, collection year, details for partial consent validation ("Consent Notes"), patient age at sample collection, reported race, percentage of off-target human reads, overall HPV status (“unclear” indicates a high fraction of human reads, “qPCR filter” indicates a low amplified DNA concentration), HPV genotype assignments (using a 20% read fraction threshold and other standard criteria defined in the Methods), percentages of specific HPV genotype reads, previous archived DNA genotyping results (based on RFLP analysis), amplified DNA concentrations (quantified by qPCR after gel extraction), median and maximum sizes among human-aligned reads (calculated from paired-end reads using Picard), paired sample IDs (based on provided annotations, QC Array IBD calculations, or both), QC Array call rate (a QC measure for the sample), primary super-population assignments (based on >50% estimated contributions, using ADMIXTURE), mixed super-population assignments (based on >20% estimated contributions, ADMIXTURE), distance-based bootstrap super-population assignments (with confidence >95%), HPV L1 amplicon sequencing barcode, run information (run number: flowcell ID: lane number), and total HPV L1 amplicon sequencing reads (combined between lanes).