For chromosomes showing subclonal copy number variation, we identified and phased mutations linked to nearby heterozygous germline SNPs.
For haplotype phasing, we attempted to phase mutations that are sufficiently close together to be spanned by single read pairs.
In addition to phase variation, high mutation rate and homologous recombination [ 7, 8], the R-M system diversity has been proposed to contribute to the genetic variation of the bacteria [ 9, 10].
In N. meningitidis, HmbR is subject to phase variation via frameshift mutations [ 50], and about half of all clinical isolates express HmbR [ 51].
We assumed that microsatellite loci follow a two-phase mutation model (intermediate between the IAM and SMM models) with 70% single-step mutations and 30% multiple-step mutations.
Significance of the neutrality test was evaluated by simulations implemented in BOTTLENECK [71] performed under the two-phase mutation model (TPM) with one-step mutations occurring at a frequency of 95% of the total.
For each generated data set, using the program Bottleneck version 1.2.02, we performed a Wilcoxon sign-rank test to determine whether a significant number of loci featured a heterozygosity excess, which is indicative of a recent botteneck event, assuming a two-phase mutation model (TPM; model of microsatellite mutation; [20]).
The phase mutation may result in the concave-convex change of mathematical surface.
We assumed that microsatellite loci follow a two-phase mutation model with 70% single-step mutations and 30% multiple-step mutations.
We used a two-phase mutation model and ran the analysis three times, with the percentage of stepwise mutations set at 95%, 90 % and 80, respectively.
Because bottlenecks can create false positive outliers, both fiber and linseed groups were analyzed with BOTTLENECK v.1.2.02 assuming the two-phase mutation model proposed for microsatellite data [ 38].
