Illumina MiSeq short read-sequencing results of the libraries constructed from MspJI-digested and physically sheared DNA. The sorted alignment was visualised using the Tablet viewers. (a) Alignment results of Φ29 enzyme-amplified Agro gDNA-derived reads and physically sheared Agro gDNA-derived reads to the reference Agrobacterium genome sequences for the 1,000-1,250 and 2,000-2250 kb regions of the circular and linear chromosomes. (b) Alignment results of the Arabidopsis genome with the MspJI-enzymatic fragmentation and physical shearing methods. Read coverage depth for the 10,000-10,250, 20,000-20,250 and 30,000-30,250 kb regions of chromosome 1 was visualised.