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Figure S3. Indiscriminate(indis) read and discriminate(dis) mapping qualities. Quality scores taken from mapping all reads to a reference with minimap2. Discriminate scores are from reads that have passed through the pipeline filtering thresholds and are determined to be reads specific to the reference. The indiscriminate are other reads that were likely to be host and/or contamination. (PDF 12 kb)

Figure S4. Each species identified by minimap2 mapping showing total bases over number of reads as proportions of total bacterial bases (centrifuge) and total bacterial reads (centrifuge) respectively. Species detections below the 0.1 proportion (i.e. less than 1%) of bases threshold are dots and species detections above the 0.01 proportion threshold are crosses. Culture negative controls are red and Culture negative positive samples are blue. Shows shortened axis of below threshold hits. (PDF 13 kb)

Figure S2. Each species identified by centrifuge showing total bases over number of reads as proportions of total bacterial bases and total bacterial reads respectively. Species detections below the 0.1 proportion (i.e. less than 10%) of bases threshold are dots and species detections above the 0.1 proportion threshold are crosses. Culture negative controls are red and Culture negative positive samples are blue. (PDF 25 kb)

Figure S1. Bases classified total or target over centrifuge score. Each sample has two lines of the same colour. The top line is total bacterial bases identified by centrifuge over the score threshold used. The second lower line is the validated detected species/infection for the sample (Target). As the score threshold increases, the number of total classified bases reduces at a great rate than the target bases, until a plateau and diminishing returns at approximately 150. (PDF 15 kb)

Figure S5. Batch job duration times in minutes sample report taken from Nextflow. Using sample 354a as a representative for the bioinformatic analysis. (A) Batches were run over a heterogeneous SLURM cluster with variable node CPU speeds affecting Albacore performance. (B) Batches were run on a single machine with an Nvidia GTX 1050ti graphics card using guppy v0.3.0 for basecalling. (PDF 280 kb)

Cattle have expanded the KIR gene repertoire, a polymorphic and polygenic im- munoglobulin family that encode Natural Killer cell receptors specific to MHC class I ligands. In humans, KIR are important mediators of innate immunity to viral pathogens such as HCV and HIV, and there is potential for exploiting cattle KIR diversity as a means of improving animal health. Cattle KIR expansion has occurred independently to humans, the result is a cattle KIR haplotype (CKH) with a completely different gene content. Successful sequencing and assembly of the CKH using whole genome techniques has failed. To interrogate cattle KIR, their function and comparative evolution, the content of a CKH must be estab- lished, then the extent of polymorphism and gene presence/absence variation can be studied. In this project the first CKH has been sequenced and assembled using second generation sequencing of BAC clones. This has provided a reference sequence for whole genome sequence data to be aligned revealing the KIR content of different Bovidae species, including the aurochs, the ancestor to all domesticated cattle. Furthermore genome capture and enrichment was performed to determine polymorphic and polygenic KIR variation within 24 different cattle genomes. The sheep KIR haplotype (SKH) was sequenced using PacBio of BAC clones to enable comparative analysis with cattle. The CKH has expanded through block duplications resulting in 16 discrete KIR loci. The haplotype is dominated by functional inhibitory receptor genes and the attenuated remains of activating KIR. Predicted similarity between au- rochs and modern CKH suggests KIR blocks expanded through natural selection and not artificial selection generated through centuries of domestication. Com- parative analysis of the SKH and CKH reveals that sheep have independently expanded at least five of the shared KIR that cattle have expanded. Cattle KIR are extremely polymorphic, with diversity focused within the Ig domains, regions predicted to interact with ligand. Open Access