Fig. 5

Manhattan plots from genome-wide association analysis of relative abundance of Peptoclostridium spp. (A) and relative abundance of Treponema spp. (B). Figure C shows a closer look at the association analysis of SNPs in Bos taurus autosome 1 (BTA1) with relative abundance of Treponema spp. The red line represents the genome-wide significance (Bonferroni corrected, so 0.05 divided by the number of SNPs) and the blue line represents the suggestive threshold (Bonferroni corrected, so 0.1 divided by the number of SNPs). In these plots, genomic coordinates are shown along the x-axis (ordered by chromosome and position in base pairs), and the negative logarithm of the association p-value for each SNP is shown on the y-axis. X-axis labels in A and B correspond to the chromosome number while in C correspond to SNP position (in base pairs) within chromosome 1