Placement Of Reads

For each pair of end sequences

For each fosmid

All paired-end alignment combinations were scored using a 13-point in-house ordinal scale for placement.

In addition to identifying the longest and most identical alignments of allelic proportions, the placement score strongly favored concordant positions over discordant ones helping to avoid false positive rearrangements due to recent segmental duplications or gene conversion events between non-allelic sites within the genome.

To add additional stringency for the detection of putative rearrangements, we required discordant alignments (insert size <76.5 kb or >277 kb and/or mis-oriented ends) to be