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Table 1 The 21 PEM patterns with their corresponding SV type

From: The fine-scale architecture of structural variants in 17 mouse genomes

PEM pattern Brief description SV type
H1 Deletion of unique sequence Simple
H2 Deletion of repeat sequence (for example, LINE, SINE, ERV) Simple
H3 Deletions separated by small normal copy (Del+Nml+Del) Simple
H4 Typical inversion Simple
H5 Inversion co-occurring with deletion(s) Complex
H6 Insertion of unique sequence (de novo sequence) Simple
H7 Insertion of repeat sequence (for example, LINE, SINE, ERV) Simple
H8 Tandem duplication Simple
H9 Inverted tandem duplication Complex
H10 Dispersed copy number gains Simple
H11 Deletion or inversion within copy number gain Complex
Q1 Deletion due to microsatellite size polymorphism Simple
Q2 Deletion of unique sequence co-occurring with insertion Complex
Q3 Deletion of repeat sequence co-occurring with insertion Complex
Q4 Large deletion Simple
Q5 Linked small gain causing a false deletion Simple
Q6 False deletion due to retrotransposed pseudogene False
Q7 Deletion due to VNTR VNTR
Q8 Inversion co-occurring with insertion Complex
Q9 Inverted linked small gain causing a false inversion Simple
Q10 False inversion due to inverted retrotransposed pseudogene False
  1. ERV, endogenous retrovirus; VNTR, variable number tandem repeat.