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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells

Fig. 3

The frequency of sequencing errors is highly predictable across samples within a single lane. (a) Artificial data from a hypothetical sequencing lane with read numbers for one mother barcode and an associated daughter barcode, derived by sequencing error, in ten samples. Read numbers for mother and daughter barcode are either plotted as a function of sample ID (left panel) or against each other (right panel). b Examples of the read counts of three potential mother barcodes and of one particular spurious barcode plotted against each other, for presumed correct (left panel) and incorrect (other panels) mother-daughter pairs. Each dot represents one technical replicate, lines denote the prediction based on total frequencies of mother and daughter barcodes. Note that only for one of the pairs the frequency of errors is quite predictable across the samples, strongly suggesting that the spurious barcode derives from that mother. c, d The 500 most frequent spurious barcodes were compared to all 19 mother barcodes and the presumed mother was selected based on predictability of sequencing errors across samples by visual inspection. The number of nucleotide sequence differences was determined for each presumed mother-daughter pair (c, left panel) and for every other possible pair (c, right panel). For the presumed mother-daughter pairs the fraction of reads of the daughter sequence relative to the mother sequence was also determined (d)

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