- A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. - Deletions and insertions are referred to as unbal- anced SV because they result in changes in the length of the genome. - Full list of author information is available at the end of the article. - CNV cover about 4.5–9.8% of the human genome [13] and are associated with many Mendelian disor- ders [12]. - Girirajan et al. - Nandolo et al. - A vast majority of the CNV (96.6%) were losses. - The distribution of the lengths of the CNV for each population are shown in Fig. - A summary of the descriptive statistics of the CNV for the populations are given in Table 1. - The rest of the genes were in CNV that were highly differ- entiated across all populations.. - Plots of the CNVR for each breed (with more than 2 ani- mals) are given in Supplementary Figures 12 to 40 (Add- itional file 2). - Descriptive statistics of the CNVR for each population are given in Supplementary Table 3 (Add- itional file 1) while a distribution of CNVR by size and populations is given in Fig. - Over 92% of the CNVR were copy losses. - There was a wide variation in the number and sizes of the CNVR between and among. - A list of the global CNVR is given in Supplementary Table 4 (Additional file 1) and a summary is given in Table 2. - The lo- cations of the global CNVR are given in Fig. - Overall, the CNVR covered about 59.2 Mb of the goat genome. - 2 Distribution of the sizes of CNV for each population by CNV state. - [18] showed that CNVR cover approximately 262 Mb of the goat gen- ome. - Most of the CNVR (>. - Higher enrichment scores imply higher overrepresentation of the genes in the gene set for the gene enrichment term [46]. - 5 Location of the CNVR for the 29 autosomes by population. - Some of the CNV displayed large differences between populations, suggestive of population-specific selective pressures.. - A large proportion of the global CNVR identified in this study (65.1%) are within the CNVR reported by Liu et al. - Yamano et al. - The rest of the colours for copy loss for each of the five populations (magenta for Boer. - Zajkowska et al. - Goats tend to be active during some parts of the day only [67], and this varies with season [67], suggesting a. - This study presents the first fine CNV map of the Afri- can goats based on WGS data. - [70], Cardoso et al. - 7 Location of the global CNVR across the 29 autosomes. - A list of the breeds, populations and samples sizes used in the analysis is given in Table 4.. - 8 Distribution of the CNVR. - 2) point of application of the lower SV length cut-off point (before or after mer- ging Manta and LUMPY SV). - 3) stringency of the SV call filters (low, medium, and high stringency). - SV longer that 3 Mb were also Table 3 Functional annotation clusters of the genes found in the global CNVR based on analysis in DAVID. - Visualization of the SV was done using R [81] package circlize version . - Read count values were corrected for size of the consen- sus CNV, batch effect, variable GC content and genomic mappability as described by Liu et al. - Regional and batch effect correction was done by computing reads per kb per million mapped reads (RPKM) as described by Table 4 List of the breeds used in the analysis. - 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