Table 4 Comparison of the parameters of SNVHMM before and after training on lobular breast cancer (LBC) data and MDS RNA_seq data for threshold of mapping quality 50 and base quality 20

π

initial

(0.904233 0.499051 0.090499)

(0.904233 0.499051 0.090499)

(0.904233 0.499051 0.090499)

trained

(0.001199 0.984717 0.014086)

(0.000001 0.999831 0.000170)

(0.988258 0.011743 0.000001)

u

initial

(0.999023 0.508543 0.000123)

(0.999023 0.508543 0.000123)

(0.999023 0.508543 0.000123)

trained

(0.904833 0.466663 0.151255)

(0.897743 0.509801 0.165214)

(0.904233 0.544121 0.090499)

A

initial

$\left(\begin{array}{ccc}\hfill 0.848400\hfill & \hfill 0.072800\hfill & \hfill 0.078800\hfill \\ \hfill 0.087570\hfill & \hfill 0.838210\hfill & \hfill 0.074300\hfill \\ \hfill 0.085100\hfill & \hfill 0.075600\hfill & \hfill 0.839300\hfill \end{array}\right)$

$\left(\begin{array}{ccc}\hfill 0.848400\hfill & \hfill 0.072800\hfill & \hfill 0.078800\hfill \\ \hfill 0.087570\hfill & \hfill 0.838210\hfill & \hfill 0.074300\hfill \\ \hfill 0.085100\hfill & \hfill 0.075600\hfill & \hfill 0.839300\hfill \end{array}\right)$

$\left(\begin{array}{ccc}\hfill 0.848400\hfill & \hfill 0.072800\hfill & \hfill 0.078800\hfill \\ \hfill 0.087570\hfill & \hfill 0.838210\hfill & \hfill 0.074300\hfill \\ \hfill 0.085100\hfill & \hfill 0.075600\hfill & \hfill 0.839300\hfill \end{array}\right)$

trained

$\left(\begin{array}{ccc}\hfill 0.567581\hfill & \hfill 0.325414\hfill & \hfill 0.107006\hfill \\ \hfill 0.061140\hfill & \hfill 0.864239\hfill & \hfill 0.074624\hfill \\ \hfill 0.044694\hfill & \hfill 0.257290\hfill & \hfill 0.698019\hfill \end{array}\right)$

$\left(\begin{array}{ccc}\hfill 0.412955\hfill & \hfill 0.476467\hfill & \hfill 0.110580\hfill \\ \hfill 0.159858\hfill & \hfill 0.723625\hfill & \hfill 0.116519\hfill \\ \hfill 0.112374\hfill & \hfill 0.323298\hfill & \hfill 0.564329\hfill \end{array}\right)$

$\left(\begin{array}{ccc}\hfill 0.999064\hfill & \hfill 0.000271\hfill & \hfill 0.000377\hfill \\ \hfill 0.986557\hfill & \hfill 0.013444\hfill & \hfill 0.000001\hfill \\ \hfill 1.000000\hfill & \hfill 0.000001\hfill & \hfill 0.000001\hfill \end{array}\right)$