Table 2 Sanger validation of novel SVs called by SoapAsmVar.

From: Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

Variant class

FDR

Sites

Structural variants

 Novel SVs

0.07

68

By length (bp)

 50–100

0.10

39

 101–300

0.00

9

 301–500

0.10

10

 501–1,000

0.00

10

By type

 DEL

0.17

12

 INS

0.05

56

By mechanism

 Unknown

0.04

25

 NAHR

0.22

9

 NHR

0.06

33

 TEI

0.00

1

 VNTR

NA

0

  1. DEL, deletion; FDR, false discovery rate; GATK, Genome Analysis Toolkit; INS, insertion; NA, not applicable; NAHR, non-allelic homologous recombination; NHR, non-homologous recombination; SV, structural variant; TEI, transposable element insertions; VNTR, variable number of tandem repeats.
  2. In total 68 novel variants were subjected to validation and the FDR was stratified by length, type of indel and formation mechanism.
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