Fig. 7

Extremely small negative gap length for in silico map of scaffold 81. Two XMAP alignments for in silico map of sequence scaffold 81 are shown. Consensus genome maps (blue with molecule map coverage shown in dark blue) align to the in silico maps of scaffolds (green with contigs overlaid as translucent colored squares). Sequence scaffolds 79–83 were placed within ChLG 5 and sequence scaffolds 99–103 were placed with ChLG 7 by the T. castaneum genetic map. a Half of the in silico map of sequence scaffold 81 aligns with its assigned ChLG (black arrow). b The other half aligns with ChLG 7 (red arrow) producing a negative gap length smaller than -20 kb. The alignment that places sequence scaffold 81 with ChLG 7 disagrees with the genetic map and was manually rejected for Tcas5.2