Fig. 9

Optical map (BtOM1.0_chr1) reveals a 79 Kb sequence assembly as being transposed and inverted in UMD3.1_chr1. (Top) Alignment shows an unaligned 79 Kb segment (pink bars) within the optical map and a corresponding gap in the sequence. (Middle) Same 79 Kb segment within the UMD3.1 build but apparently transposed to 60,578,754 bp and inverted. Accordingly, there is a 79 Kb gap in the optical map. (Bottom) Illumina paired-end Dominette L1 sequence data, aligned to UMD3.1 corroborates sequence misjoining points (red arrows) at 60,578,000 bp and 60,664,500 bp. PCR experiments confirms that the 79 Kb segment should be placed between 637,768 and 648,912 on chromosome 1 (data not shown). Paired-end reads mapped to UMD3.1 showing correct orientations with both ends mapped are named an intact pair (blue tracks). When only one end is mapped, or mapping shows wrong orientation, or revealing discordant distances between mapped read pairs, these events are termed broken pairs. Reads of a broken pair that map to a unique location against the reference are colored green or red, according to whether they mapped in the forward, or reverse, orientation respectively