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Table 2 Summary of indels and SVs called in the founder animals of three trios by WGS

From: Low incidence of SNVs and indels in trio genomes of Cas9-mediated multiplex edited sheep

Variants

#25

#28

#A9

Indels

 Called by GATK+Samtools

2,225,916

 SNVs that specific for each founder and filtering SNVs existed in the reads with alternative alleles (< 25%), and the read depth in founders < 3 within a trio

57

64

40

 The PL scores for each genotype in founders should be > 20, 0 and > 0, the PL scores for each genotype in both parents should be 0, > 20 and > 20

56

58

39

 Manual examination to remove mis-alignment or miscall INDELs

25

26

17

SVs

 (1) Called by BreakDancer

2491

3198

3348

  After removal of common SVs in every two founders, and the read depth < 50%

8

3

15

 (2) Called by Lumpy

109

94

132

  After removal of scaffold SVs

3

4

1

 (3) Called by CNVcaller

1547

1124

1144

  Candidate de novo CNVs

6

3

4