Here is the results

0Mb 5Mb 10Mb 15Mb 20Mb 25Mb 30Mb 35Mb 40Mb 45Mb 0 50 100 Gene Density 100Kb 0 TE 2000 0 SNP Telomere NLR PAV Inversion Synteny Type ZS97 MH63 Chr01 R498 ZS97 MH63 Chr02 R498 ZS97 MH63 Chr03 R498 ZS97 MH63 Chr04 R498 ZS97 MH63 Chr05 R498 ZS97 MH63 Chr06 R498 ZS97 MH63 Chr07 R498 ZS97 MH63 Chr08 R498 ZS97 MH63 Chr09 R498 ZS97 MH63 Chr10 R498 ZS97 MH63 Chr11 R498 ZS97 MH63 Chr12 R498
Translocation Inversion Synteny MH63 Chr01 ZS97 Chr01 R498 Chr01 Chr02 Chr02 Chr02 Chr03 Chr03 Chr03 Chr04 Chr04 Chr04 Chr05 Chr05 Chr05 Chr06 Chr06 Chr06 Chr07 Chr07 Chr07 Chr08 Chr08 Chr08 Chr09 Chr09 Chr09 Chr10 Chr10 Chr10 Chr11 Chr11 Chr11 Chr12 Chr12 Chr12

If you want to get such a picture with comprehensive information, you can try our perl version of the script and enter the following command in the command line:

GenomeSyn -t 3 -g1 ../data/MH63_RS3.fa -g2 ../data/ZS97_RS3.fa -g3 ../data/R498_Final_Version2.fasta -cf1 ../data/MH63RS3vsZS97RS3.delta.filter.coords -cf2 ../data/MH63RS3vsR498.delta.filter.coords -cen1 ../data/MH63_centromere.bed -cen2 ../data/ZS97_centromere.bed -cen3 ../data/R498_centromere.bed -tel1 ../data/MH63_telomere.bed -tel2 ../data/ZS97_telomere.bed -tel3 ../data/R498_telomere.bed -TE1 ../data/MH63_repeat.bed -TE2 ../data/ZS97_repeat.bed -PAV1 ../data/MH63_PAV.bed -PAV2 ../data/ZS97_PAV.bed -NLR1 ../data/MH63_NLR.bed -NLR2 ../data/ZS97_NLR.bed -r MH63 -q1 ZS97 -q2 R498 -GD1 ../data/MH63_nonTEgene.gff3 -GD2 ../data/ZS97_nonTEgene.gff3 -GD3 ../data/R498_IGDBv3_coreset.gff -GC1 ../data/MH63_RS3_GC_1000.bed -GC_win 10000

Download your example data.