Copy number analyses in representative core elements. Mapped aCGH log2 values in the core elements that compare MSM (musculus subspecies group) or BLG2 (musculus) with B6 (domesticus) are shown by green and magenta diamonds, respectively. Relative copy numbers estimated by qPCR with unique probes using genomic DNA from BLG2, MSM, and B6 are shown by X in the same colors. Average aCGH values for MSM compared with B6, and for BLG2 compared with B6 in the relevant regions are shown by red and green lines, respectively. (A) Mapping of aCGH log2 values to a representative CNV-type core element (core element 541). Three relative values obtained by qPCR plotted around 1.0 (indicated by X), which shows that the copy number of core element 541 is higher in BLG2 and MSM than in B6. Primers for qPCR were designed for three regions of core element 541 (320–456, 1599–1693, and 2050–2162) (Additional file 5: Table S5). (B) Mapped aCGH values on a representative constant-type core element (core element 454) were distributed around zero. Furthermore, all the qPCR values plotted around zero (indicated by X). These results showed no CNV between B6 and MSM within core element 454.