Additional file 2 of A comprehensive atlas of nuclear sequences of mitochondrial origin (NUMT) inserted into the pig genome

Additional file 2: Table S5. Information on the NUMT identified in the assembled genomes. Table S6. List of all NUMT sequences identified in the assembled genomes with LAST alignment information. Table S7. Comparison at the chromosome/scaffold level between NUMT identified in Sscrofa11.1 and Sscrofa10.2 reference genomes. Table S8. Matrix of orthologous NUMT regions over all Suinae investigated assembled nuclear genomes. The matrix below the diagonal contains the number of NUMT regions orthologous between the two genomes; the diagonal of the matrix reports the total number of regions found in the genome and the number of regions belonging to portions of the genome not aligned with Sscrofa11.1. The matrix above the diagonal contains the number of regions from genome A not found in genome B and vice versa. The acronyms of the reference genomes are explained in Additional file 2 Table S5. Table S9. List of all non-redundant NUMT regions found in the assembled genomes with presence/absence in all other assembled genomes. NUMT regions that could not be reconducted to a position in Sscrofa11.1 were not included. The first six columns contain the unique NUMT region ID and its coordinates in Sscrofa11.1. For NUMT regions absent in Sscrofa11.1 the coordinates of the insertion point are reported instead. The remaining columns refer to the information for the unique NUMT region in the assembled genomes: the reported information for each genome, when available, were the ID and coordinates of the corresponding NUMT region, along with its status, defined as follows: CORRESPONDING, if the genome contains the NUMT region; COMPATIBLE SEQUENCE, if the genome aligns with Sscrofa11.1 on the NUMT region coordinates, and the corresponding sequence in the other genome was not annotated as NUMT by the NUMT discovery pipeline; PRIVATE, if the alignment between the assembled genome and Sscrofa11.1 contains gaps corresponding to the NUMT region coordinates in one of the two genomes, meaning that the NUMT insertion happened only in one of the two genomes, and the NUMT can be therefore considered as polymorphic. Each status column contains the information for Sscrofa11.1 on the left side and the other genome on the right side. Table S10. List of all novel NUMT identified by mining WGS datasets. Breakpoints belonging to the same NUMT insertion are grouped with the same NUMT region ID. Table S11. Frequency of the carriers of novel NUMT regions estimated from WGS datasets within breed/population and species. For each NUMT region, number of WGS datasets and their percentageof the carriers is reported. Table S12. Genotype information obtained by PCR analyses of some polymorphic NUMT in several pig breeds and populations. The number of pigs having the three genotypesis reported. Table S13. Frequency of the carriers of all non-redundant NUMT regions found in assembled genomes estimated from WGS datasets within breed/populations and species. For each NUMT region, number of WGS datasets and their percentage of the carriers is reported. Table S14. Information on NUMT derived from the assembled genomes and WGS datasets with age estimation, presence/absence in the assembled genomes and WGS datasets divided by species and geographic origin of the pigs. Table S15. Comparative age estimation of NUMT regions assigned to the age classes 10–55 Mya and > 55 Mya, based on different mutation rates. Table S16. Annotation of the genomic regions where the NUMT regions are inserted.