Fig. 2: Analysis of supplementary alignments.

a Venn diagrams of the comparisons between trios of direct sputum (dWGS), enriched sputum (eWGS), culture WGS. Amount and percentage of exclusive and common variants are denoted. Blue and orange Venn diagrams represent comparisons of variant calls from default unfiltered bams (including supplementary alignments and filtered bams, respectively. b Comparison of the amount of supplementary alignments between direct (sputum dWGS and culture WGS, light purple) and enriched sputum samples (eWGS, dark purple) in all 61 paired-samples. Median (M) and the total amount of samples (n) are shown. Asterisk (*) highlights a significant p-value (Wilcox test, p-value = 0.0002049). Data are presented as box-plots: centre line represents the median, upper bound located at 75th percentile, lower bound at 25th percentile, whiskers at minimum and maximum values and the outliers. Each dot represents one sample. c On the left there is the comparison of the discrepant SNPs exclusive in sputum, either dWGS and eWGS, before and after filtering supplementary alignments. Colours stand for variant calls from bams before discarding supplementary alignments (blue) and after discarding them (orange). The x-axis is discontinued. The right part shows the percentage of supplementary alignments in sputum files, either dWGS (light purple) and eWGS (dark purple). Plot c contains 32/61 pairs, the 16 ones containing a higher percentage of supplementary alignments in each eWGS and dWGS. Samples are ordered from the highest to the lowest amount of supplementary alignments. The complete version containing the 61 pairs can be seen in Supplementary Fig. 3. d Correlation between the percentage of supplementary alignments and the amount of SNPs removed when discarding supplementary alignments from sputum bam files (represented as SNP difference and calculated as follows: discrepant SNPs exclusive in sputum in Default Bams—Filtered Bams). Colours represent whether the sputum samples have been sequenced directly (light purple) or previously enriched (dark purple). Regression lines, Pearson correlation coefficients (one-side) (Corr) and p-values are shown in the plot. Source data are provided as a Source Data file.