Do you have someone who has an Illumina machine that you could ask for typical settings for e and E (base error rate)? For human, the rate of mutation (SNPs) is 1/1000, while for indels it is ~1/10000.
If you are using this tool, sequencing is your domain. e/E are the per base mean error rate, r is the rate of mutation, R is the fraction of mutations that are indels, and X controls the indel length distribution (probability of extending an indel).
