Additional file 2 of Single-cell sequencing of the small and AT-skewed genome of malaria parasites

Additional file 2: Table S1. GC content of 5 base windows in the P. falciparum genome. Table S2. Primer and probe design for droplet digital PCR. Table S3. Correlation between ddPCR gene copy concentration and sequencing depth of ddPCR target. Table S4. Overall sequencing read output and percentage of aligned reads to P. falciparum genome. Table S5. Proportion of reads that contain the MALBAC primer common sequence and their alignment to specific genomic regions. Table S6. CNVs detected by LUMPY in all samples (single cell and Dd2 bulk). Table S7. CNVs detected by Ginkgo in all samples (single cell and Dd2 bulk). Table S8. The number of single cell samples processed at each analysis step. Table S9. DNA yield after MALBAC amplification. Table S10. Primary data from ddPCR detection: calculation of uniformity score and Pfmdr1 copy number. Table S11. Coefficient of variation of normalized read abundance in each sequenced sample. Table S12. The equality of CVs in normalized read abundance for sequenced samples. Table S13. Spearman correlation coefficient of all sequenced samples. Table S14. Comparison between experimental conditions of MALBAC and MDA-amplified single cell samples. Table S15. The coefficient of variation of normalized read abundance in MDA amplified samples. Table S16. Coverage comparison after downsampling to 300,000 reads. Table S17. Spearman correlation coefficient of MDA amplified samples. Table S18. Detection of true CNVs in single cell genomes by discordant/split read or read depth analysis. Table S19. Precision and sensitivity of CNV detection. Table S20. Single cell CNVs detected by both discordant/split read and read depth analysis (excluding true CNVs presented in Table 5). Table S21. Detection of known SNPs in resistant genes in Dd2 bulk sample. Table S22. Detection of known SNPs in resistant genes in single cell samples. Table S23. Subpopulation SNPs detected in single cell samples. Table S24. Pathways of genes affected by novel SNPs detected in single cell samples.