Indel calls of less than 50 bp were validated using multiplex PCR and targeted re-sequencing. We used 13 multiplex-primer combinations to capture and simultaneously amplify 172 (50%) of the previously identified indels. Primers were designed using MPprimer to capture regions of between 190 and 250 bp in size44 (sequences available upon request). The first of round multiplex-PCR amplifications was performed with tailed gene primers and was individually barcoded by a second round of PCR with pre-validated MiSeq-ready primers45, using a high fidelity polymerase (Q5 Hot Start HF, New England Biolabs). The PCR reaction conditions were as follows: Group 1, 100 ng DNA input in 25 μl PCR reaction, 95 °C for 2 min, six cycles of 98 °C for 20 s, 65 °C for 60 s, 60 °C for 60 s, 55 °C for 60 s, 50 °C for 60 s and 70 °C for 60 s, the reaction was then held at 4 °C until addition of barcoded second-round primers, followed by 19 cycles of 98 °C for 20 s, 62 °C for 15 s and 72 °C for
