Table 5.

Notation used in ‘Methods’

Symbol	Definition
$ℝ$	Set of all fragments
$\mathbb{𝔼}$	Set of all fragments from the endogenous genome
R j	a particular fragment in R, with l bases $\{r_1,\dots ,r_l\}$ and respective error probabilities $\{{\epsilon }_1,\dots ,{\epsilon }_l\}$, which are given by the per-base quality scores
E	The event that a sequencing error has occurred
D	The event that deamination has occurred
C	The event that R j was sampled from a contaminant mitochondrial genome
M	The event that R j was correctly mapped
$m_{R_j}$	Probability that R J is mismapped (P[¬M])
b e	The base from the endogenous genome
b c	The base from the contaminant genome
c	The base from the contaminant genome used by mtCont, obtained from a database
r i	The base at position i from fragment R j
ε i	The probability that base r i has a sequencing error as determined by the base caller
¬	Denotes the complement of an event (event has not occurred)
c d	Contamination rate, estimated by contDeam
c r	Contamination rate, estimated by mtCont
c c	Prior on contamination rate provided as input to endoCaller
endodist	log-normal distribution of the fragment length for the endogenous fragments
contdist	log-normal distribution of the fragment length for the contaminant fragments