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Fig. 4 | BMC Medical Genomics

Fig. 4

From: Establishing analytical validity of BeadChip array genotype data by comparison to whole-genome sequence and standard benchmark datasets

Fig. 4

Boxplot analysis of the performance metrics of GSA vs 1KG benchmark dataset when assays are classified according to A variation type (deletion (DEL), insertion (INS), single nucleotide variant (SNV)), B type of single nucleotide change (transition (TNS), transversion (TVS)), (C) frequency of the alternate allele in the 1000 Genomes (1KG) data, and (D) interrogation of a low complexity genomic region (microsatellite region (MicroSat), RepeatMasker region (RepMask), or simple repeat (SimRep)). The performance metrics measured and plotted as boxplots for each class/panel are concordance (blue), sensitivity (coral), specificity (green) and positive predictive value (PPV) (orange)

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BMC Medical Genomics

ISSN: 1755-8794

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