Given this, although the assembled fusion sequence is correct, Barnacle cannot decide which of the two possible breakpoint locations is correct, and if both alignment options overlap genes, both are reported.
According to the array CGH data the two breakpoints are located between RP11 247C02 and RP11 672A20 (proximal breakpoint) and RP11 758J16 and RP11 745I11 (distal breakpoint).
By repeating this procedure for all replicate datasets over a 20 bp region around the true breakpoints, we found the estimated breakpoint locations to be within 20 bp of the true values on 63% of the eight taxa datasets and on 91% of the simulations with 12 taxa, on average.
We designed short mapping PCRs around the Phex locus to refine the putative breakpoint locations, then used gap PCR to amplify a product containing the breakpoint junction.
After breakpoint identification, each segment was extracted and analyzed phylogenetically to confirm the assignment of subtype; breakpoint locations were designed relative to HXB-2.
Remarkably, only GalileoN was present at the two breakpoint junctions.
The severity of the phenotype may be owing to the complexity of the rearrangement, the breakpoint locations, and gene content.
After recombination breakpoint locations were determined, the genotype of each RIL was assigned.
Most commonly used methods for SV detection provide only approximate breakpoint locations.
Genetic Algorithm Recombination Detection (GARD) methods were also used to detect recombination and estimate breakpoint locations.
