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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