I have mapped whole genome sequences from Illumina Hiseq 2000 to the dog genome. We have mapped more than 15 genomes using BWA with default parameters. But we noticed a strange pattern in mapping of some genomes. These genomes had no reads mapped to some repetitive regions, the only common pattern that we saw was that all genomes were sequenced on the same flow cell. The other genomes sequenced on other flow cells had good coverage in the repetitive regions. Wondering what could be the cause for this ? Thank you for any explanation.