Table 5 Notation used in ‘Methods’
From: Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA
Symbol | Definition |
|---|---|
\(\mathbb {R}\) | 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 |