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Table 1 12 types of genotype transitions that SIEVE is able to identify, with their interpretation as mutation events. The genotype transitions correspond to possible changes of genotypes on a branch from the parent node to the child node. If any of these events occurs on independent branches of the phylogenetic tree, it is also considered as a parallel evolution event. For detailed explanations of the mutation events, see the “Methods” section

From: SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data

Genotype transition

Mutation event

\(0/0 \rightarrow 0/1\)

Single mutation

\(0/0 \rightarrow 1/1\)

Homozygous coincident double mutation

\(0/0 \rightarrow 1/{1}^{\!\prime }\)

Heterozygous coincident double mutation

\(0/1 \rightarrow 0/0\)

Single back mutation

\(1/1 \rightarrow 0/1\)

Single back mutation

\(1/{1}^{\!\prime } \rightarrow 0/1\)

Single back mutation

\(1/1 \rightarrow 0/0\)

Double back mutation

\(1/{1}^{\!\prime } \rightarrow 0/0\)

Double back mutation

\(0/1 \rightarrow 1/1\)

Homozygous single mutation addition

\(0/1 \rightarrow 1/{1}^{\!\prime }\)

Heterozygous single mutation addition

\(1/{1}^{\!\prime } \rightarrow 1/1\)

Homozygous substitute single mutation

\(1/1 \rightarrow 1/{1}^{\!\prime }\)

Heterozygous substitute single mutation