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\section{Methods}  \subsection{Data simulation}  \bigskip  We used fastsimcoal2 \cite{Excoffier_2013} to simulate ancestral trees and $3000$ haplotypes of $4000$ equispaced SNVs in a $2$ million base pair(Mbp) genomic region with recombination rate $1\times10^{-8}$per base pair per generation in a haploid population of constant effective size, $N_e=6200$ \cite{Tenesa_2007}. We then randomly paired these 3000 haplotypes into 1500 individuals.   Once we randomly paired haplotypes into 1500 individuals, the disease status was assigned to the individuals based on randomly sampled susceptibility SNVs from the middle region of $950kbp-1050kbp$. For the disease susceptibility variants, the number of copies of the derived allele increases disease risk according to a logistic regression model: