Additional file 1 of Detecting selection in low-coverage high-throughput sequencing data using principal component analysis
Creators: name: Meisner, Jonas
name: Albrechtsen, Anders
name: Hanghøj, Kristian
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Figure S1: Mean depth of coverage of the low coverage data from the 1000 Genomes Project with East Asian and European ancestries used for selection scans. Figure S2: PCAngsd results on the high quality genotype dataset of the Asian populations in the 1000 Genomes Project. PCA plot of the four Asian populations showing the separation of Northern and Southern Asia on PC1 and PC2 separating KHV and CDX (A). QQ-plot of the test statistics, including PCAngsd-S2 statistics before and after genomic inflation correction (B). Manhattan plot of the selection scan of PC1 (C) and PC2 (D) based on the PCAngsd-S1 statistic and PCAngsd-S2 (E) of both PCs. Manhattan plots from PCAngsd-S2 has been corrected for genomic inflation. Red horizontal line is the Bonferroni adjusted significance level. Figure S3: PCAngsd results on the high quality genotype dataset of the European populations in the 1000 Genomes Project. PCA plot of the four European populations showing the separation of Northern and Southern Europe on PC1 (A). QQ-plot of the test statistics, including PCAngsd-S2 statistics before and after genomic inflation correction (B). Manhattan plot of the selection scan based on the PCAngsd-S1 (C) and PCAngsd-S2 (D) test statistics along PC1. Manhattan plots from PCAngsd-S2 has been corrected for genomic inflation. Red horizontal line is the Bonferroni adjusted significance level. Figure S4: QQ-plots and Manhattan plots of the selection statistics from FastPCA [1] and pcadapt [3] applied to the four East Asian populations obtained. Red horizontal line is the Bonferroni adjusted significance level. pcadapt has been corrected for genomic inflation. CG standard: Called genotypes from low-coverage data with a genotype quality threshold on 20. Figure S5: QQ-plots and Manhattan plots of the selection statistics from FastPCA and pcadapt applied to the four European populations obtained. Red horizontal line is the Bonferroni adjusted significance level. pcadapt has been corrected for genomic inflation. CG standard: Called genotypes from low-coverage data with a genotype quality threshold on 20. Figure S6: PCA plot, QQ-plots and Manhattan plots of the selection statistics obtained from PCAngsd, FastPCA and pcadapt applied to a European (CEU), Asian (CHB), and African (AFR) population. Red horizontal line is the Bonferroni adjusted significance level. Only one PCA plot is shown as they were all identical. pcadapt has been corrected for genomic inflation. HQG: High quality genotype data. Figure S7: Read length bias in the low-coverage sequencing data of the East Asian populations. (AB) PCA plots of the data only filtered using a callability filter, where in (A) individuals are colored by population, and (B) displays the individuals colored by sequencing read length. (C-D) PCA plots of the data filtered by a callability filter and corrected for read length bias. Figure S8: No read length bias in the low-coverage sequencing data of the European populations. (A-B) PCA plots of the data filtered using a callability filter, where in (A) individuals are colored by population, and (B) displays the individuals colored by sequencing read length. Figure S9: PCA plot, QQ plots and Manhattan plots of the selection statistics obtained from PCAngsd applied to the four East Asian populations for SNPs called from the low-coverage sequencing data using ANGSD [2]. The called SNPs have additionally been filtered using a callability filter and corrected for readlength bias. Red horizontal line is the Bonferroni adjusted significance level. Figure S10: PCA plot, QQ plots and Manhattan plots of the selection statistics obtained from PCAngsd applied to the four European populations for SNPs called from the low-coverage sequencing data using ANGSD [2]. The called SNPs have additionally been filtered using a callability filter. Red horizontal line is the Bonferroni adjusted significance level. Figure S11: Downsampling to 0.5 fraction of the reads of the low-coverage sequencing data. PCA plot, QQ plots and Manhattan plots of the selection statistics obtained from PCAngsd applied to the four East Asian populations for SNPs called from the downsampled low-coverage sequencing data using ANGSD [2]. Red horizontal line is the Bonferroni adjusted significance level. Figure S12: Downsampling to 0.5 fraction of the reads of the low-coverage sequencing data. PCA plot, QQ plots and Manhattan plots of the selection statistics obtained from PCAngsd applied to the four European populations for SNPs called from the downsampled low-coverage sequencing data using ANGSD [2]. Red horizontal line is the Bonferroni adjusted significance level. Figure S13: PCA plots from PCAngsd based on the low-coverage sequencing datasets with individuals colored by their estimated individual allele frequencies in the top hits for the East Asian and European populations, respectively. The individual allele frequencies reveal the direction of the PC-based selection signals in regards to the reference allele. (A) shows the top significant hit on PC1 for the East Asian populations for the LILRA3 region (rs434124), and (B) shows the top significant hit on PC1 for the European for the LCT/MCM6 region (rs6754311).