Supplemental material for Lobo et al. 2021

Supplemental material for AK Lobo, LL Traeger, MP Keller, AD Attie, FE Rey, KW Broman, Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice.

Table S1: Expected proportion of A microbiome reads assuming it is a mixture of two genomic DNA samples as function of the genotypes of the two samples.

Table S2: Read counts in microbiome sample DO-360 broken down by observed SNP allele and by the genotype of genomic DNA sample DO-360.

Table S3: Read counts in microbiome sample DO-360 broken down by observed SNP allele and by the genotype of genomic DNA sample DO-370.

Table S4: Read counts in microbiome sample DO-358 broken down by observed SNP allele and by the genotypes of genomic DNA samples DO-358 and DO-344.

Table S5: Read counts in microbiome sample DO-101 broken down by observed SNP allele and by the genotypes of genomic DNA samples DO-101 and DO-102.

Table S6: Read counts in microbiome sample DO-111 broken down by observed SNP allele and by the genotypes of genomic DNA samples DO-111 and DO-112.

Table S7: Read counts in microbiome sample DO-191 broken down by observed SNP allele and by the genotypes of genomic DNA samples DO-191 and DO-146.

Figure S1: Illustration of genome reconstruction. A: Inferred diplotype across the genome for mouse DO-359, with an arbitrary choice of phase. (For example, if there is a region of homozygosity, the haplotypes above can be swapped relative to the haplotypes below.) White indicates unknown (no diplotype had probability >0.5). B: Heat map of the diplotype probabilities for mouse DO-359 along chromosome 16. Only diplotypes that achieved probability > 0.25 are shown.

Figure S2: For selected microbiome samples, plots of their distance to each genomic sample, with distance measured by taking, among reads that overlapped a SNP where the genotyped sample was homozygous, the proportion with an allele that was discordant with the inferred SNP genotype. The sample with what should be the correct label is highlighted in dark pink. A set of low-quality DNA samples are highlighted in pale pink.

Figure S3: For selected microbiome samples, plots of the likelihood ratio test statistic vs. the estimated proportion contaminated, when considered with each of the genomic DNA samples, one at a time, with the assumption that the microbiome sample is a mixture of the correct sample and that particular contaminant. Note the change in the y-axis limits in the bottom row of panels.

Figure S4: For further selected microbiome samples, plots of the likelihood ratio test statistic vs. the estimated proportion contaminated, when considered with each of the genomic DNA samples, one at a time, with the assumption that the microbiome sample is a mixture of the correct sample and that particular contaminant. Note the change in the y-axis limits in the bottom three rows of panels.