Additional file 6: of Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

File S2. A summary of log-likelihood scores from the nQuire programme, showing the percent of heterozygous sites retained after the denoise step, the score for the free, diploid, triploid, and tetraploid models, and the differences between the diploid, triploid, and tetraploid models and the free model. The “Allreads_nQuire” tab summarises the results for when all decontaminated reads were mapped back to the genome assemblies, “Repfree_selfmaps_nQuire” summarises the results for when repetitive reads were removed from the read libraries (all reads were mapped to the repeats assembled by dnaPipeTE, and read pairs where neither read mapped to the repeats were extracted and considered “repeat free”) and mapped back to the assemblies, and “Repfree_reads_BUSCO_nQuire” summarises the same repeat free mappings, but restricted only to the shared 740 BUSCO genes. (XLSX 12 kb)