Data release: Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration

Source data used in the publication: Berger et al. (2021) - Provisional title: 'Whole-genome sequencing of Schistosoma mansoni reveals extensive diversity with limited selection despite mass drug administration'. These data were used to generate all figures used in the publication and all files are organised and labelled specifically to run with the custom code that uses these data can be found at: http://doi.org/10.5281/zenodo.4975908. 

File descriptions:

SOURCE DATA.zip - All source data for all figures. 

Figure 1b:

• supplementary_data_9.txt - Metadata

Figure 2a&b:

• 207_PCA.eigenvec - PCA eigenvectors
• 207_PCA.eigenval - PCA eigenvalues

Figure 2c:

• autosomes.mdist - PLINK distance matrix used to build the neighbour joining phylogeny

Figure 2d:

• all.pi.pixy.schools.txt - Nucleotide diversity results for each school subpopulation.

Figure 2e:

• autosomes.dxy.5kb.schools.txt - Autosomal D_XY results between school subpopulations. 
• autosomes.fst.5kb.schools.txt - Autosomal F_ST results between school subpopulations.

Figure 2f:

• admixture_all.txt - ADMIXTURE results for each sample and population sizes, column 1 represents number of populations (K), columns 3-8 represent admixture values for each population. 

Figure 3a, Supplementary figure 10a:

• sfs.csv - Site frequency spectra (allelic proportions at each frequency bin) for each school. 

Figure 3b:

• TD.all.txt - Tajima's D values calculated in 5 kb windows for each school subpopulation. 

Figure 4a, Supplementary figures 13-18: 

• ALL.MAYUGE.IHS.ihs.out.100bins.norm.txt.zip  - Normalised iHS scores for the Mayuge district parasite populations (Selscan output).

Figure 4b, Supplementary figures 13-18: 

• ALL.TORORO.IHS.ihs.out.100bins.norm.txt.zip - - Normalised iHS scores for the Tororo district parasite populations (Selscan output).

Figure 4c, Supplementary figures 13-18: 

• ALL.MAYUGEvsTORORO.xpehh.xpehh.out.norm.txt.zip - - Normalised XP-EHH scores between Mayuge and Tororo parasite populations.

Figure 4d, Supplementary figures 13-18:

• MAYUGE_TORORO_2000.windowed.weir.txt.zip - F_ST values calculated between Mayuge and Tororo populations in 2kb windows.  

Figure 4e, Supplementary figures 12a&c:

• MAYUGE_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Mayuge populations. 
• TORORO_PI.windowed.pi.zip - Nucleotide diversity values calculated in 2 kb windows for Kocoge populations (Tororo district).

Figure 5a:

• all.pi.treat.fix.txt.zip - Nucleotide diversity results for each treatment subpopulation

Figure 5b

• autosomes.dxy.5kb.treatment.txt -  - Autosomal D_XY results between clearance phenotype subpopulations. 
• autosomes.fst.5kb.treatment.txt - Autosomal F_ST results between clearance phenotype subpopulations. 

Figure 5c:

• fst.windows.2kb.treatment.txt.zip - F_ST values for comparisons between different treatment groups (Pre-treatment, post-treatment (good clearers), post-treatment (poor clearers))

Figure 5d: 

• assoc_err_binary.txt.zip - Results of binary trait association between miracidia sampled from hosts with good clearance phenotypes (where treatment appeared to be highly effective) and miracidia isolated post-treatment from hosts with poor clearance phenotypes (where miracidia are potentially derived from parasites that survived treatment.

Figure 5e:

• assoc_err_linear.txt.zip - - Results of linear regression genome-wide association study with the ERR estimates for all 198 samples, using the mean of the posterior ERR estimates from Crellen et al. (2016) as a quantitative trait.

Supplementary figure 1:

• median.coverage.txt - Normalised depth of read coverage (column 4) calculated in 25 kb windows (columns 2&3) across all samples for all chromosomes (column 1).

Supplementary figure 2a-f: 

• cohort.genotyped.txt.zip -  - Variant quality site values (used to inform variant site retention or removal). 

Supplementary figure 2g:

• hard_filtered.imiss.txt -  Per sample variant missingness (used to inform quality control).

Supplementary figure 2h:

• hard_filtered_filtindv.lmiss.txt.zip - Per site missingness (used to inform quality control).

Supplementary figure 3a, 4a, 4b:

• prunedData.eigenvec - PCA eigenvectors
• prunedData.eigenval - PCA eigenvalues

Supplementary figure 3b:

• pruned_data.mdist.csv - Distance matrix used as the basis for the neighbour joining phylogeny.

Supplementary figure 5:

• cv_scores.txt - ADMIXTURE coefficient of variation scores (column 2) for each population size (1).

Supplementary figure 6:

• *_SMC_SE.csv - SMC++ results (from 25 subsampled replicates) for each school subpopulation and outgroup samples. 

Supplementary Figure 7:

• smcpp.csv - SMC++ results for each school subpopulation and outgroup samples. 

Supplementary Figure 8a-d

• pi.per_host.txt.zip - Nucleotide diversity values for each host infrapopulation. 

Supplementary Figure 9:

• sexing.csv - inferred sex (based on differential read coverage over pseudoautosomal and Z-specific regions of the Z chromosome). 

Supplementary Figure 10b:

• sfs_res.csv - residuals for the SFS analysis in 3a/10a.

Supplementary Figure 11:

• MAYUGE_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Mayuge population in 2kb windows. 
• Tororo_TAJIMA_D.Tajima.D.2kb.txt.zip - Tajima's D values calculated for the Tororo population in 2kb windows. 

Supplementary Figures 13-18:

• genes.bed - Coordinates of gene models (S. mansoni v7 annotation).
• KOCOGE_SITE_PI.sites.pi.txt.zip - Per site nucleotide diversity values
• MAYUGE_TORORO_sites.weir.fst.txt.zip - Per site F_ST values between Mayuge and Tororo populations. 
• coverage_5kb.windows.txt.zip - Per sample depth of read coverage in 5 kb windows. Columns 4,5,6 represent the median, mean and sstev of coverage for each 5kb window (columns 2&3) along each chromosome (column 1). 
• median.sample.coverage.txt -  Median chromosomal depth of read coverage for each sample. 

Supplementary Figure 19:

• kocoge_median.ld.txt.zip -  - The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Kocoge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. 
• mayuge_median.ld.txt.zip - The decay of linkage disequilibrium with genomic distance between all sites within 50 kb for the Mayuge parasite samples. Chromosomes are shown in column 1, distance in column 2, median values in column 3. 

Misc files:

schools.list - List of samples and schools where they were sampled.