Additional file 5: of A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds

Figure S4. Genome-wide Satsuma alignments between hybrid assembly (Amel_HAv3) and Amel_4.5. A) Alignments across every chromosome. Upper plot: genome-wide GC-content is indicated with a white dashed line and local %GC is mapped across all chromosomes (10kbp non-overlapping windows; light-blue curve on y1-axis). The density of telomeric TTAGG repeats is shown on the y2-axis (10kbp non-overlapping windows; dark-blue curve with circles). Average GEM mappability scores is show on y2-axis (10kbp non-overlapping windows; grey curve). Lower plot: Amel_4.5 scaffolds (upper grey arrows) aligned against Amel_HAv3 contigs (lower black arrows). Coordinates are Mbp-scale. Colors indicate aligned blocks (blue = alignments between sequences that occur on the same chromosome in both assemblies; green = alignments between sequences that are anchored to chromosomes in Amel_HAv3 but were unplaced in Amel_4.5; yellow = alignments between sequences that have switched chromosomes). White spaces are unaligned regions. The locations of centromeric AvaI (green) and telomeric AluI (black) clusters, respectively, are marked along chromosomes. B) As in A, but for unplaced fragments. (ZIP 2983 kb)