Additional file 3.

Table S2. (a) Optical map results. Column B lists the scaffold IDs for the 295 scaffolds mapped to the 69 complete and four partial optical chromosome maps (listed in column A from largest to smallest, with the four partial chromosomes at the end). No scaffolds aligned reliably to chromosomes 53, 55, 65 and 66. Column C indicates the orientation of the scaffold sequence relative to the optical map, either end to beginning (EB) or vice versa. 'Chromosome Start' and 'Chromosome End' are calculated from the optical map data and correspond to the positions where each scaffold reliably aligns. 'Scaffold Start' and 'Scaffold End' indicate the portion of the predicted SpeI digest of each scaffold that aligns to the map. All lengths are in base pairs. Among the telomere-containing scaffolds, it is evident that the chromosome and scaffold values are not always in exact agreement with their chromosome-terminal positions due to experimental uncertainty in the optical mapping protocol. In the 18 cases (highlighted in yellow) where SOMA but not MapSolver placed a telomere-containing scaffold, the 'Chromosome Start' and 'Chromosome End' values are simply calculated from the total chromosome length and the length of the scaffold. In total, 242 scaffolds were placed by agreement between MapSolver and SOMA with no input from telomere data; 231 of these were placed by SOMA using the highest confidence MATCH algorithm, 9 using the FILTER algorithm and 2 using the SCHEDULE algorithm (see Materials and methods). Thirty-four scaffolds were placed by agreement between MapSolver, SOMA (33 MATCH, 1 SCHEDULE) and telomere position. Eighteen were placed by agreement between SOMA (9 MATCH, 7 SCHEDULE, 2 FILTER) and telomere position. One was placed on partial chromosome 73 by agreement between MapSolver, SOMA and telomere position, although the optical map position is non-terminal, presumably due to a misassembly (see Results and discussion). (b) Unmapped telomeric scaffolds. IDs of the 65 telomere-containing scaffolds that did not reliably align to a unique position on the optical map.

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Coyne et al. Genome Biology 2011 12:R100   doi:10.1186/gb-2011-12-10-r100