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Table 1 Summary of SNVs 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

SNVs #25 #28 #A9
Called by GATK 21,086,636
Founder specific SNV which were also identified by Samtools 3430 5294 3288
Filtering SNVs existed in the sheep SNP databases (n = 294, >  79 million SNPs) 3383 5252 3252
Filtering SNVs have not existed in the sheep SNP databases 2227 2696 2355
Filtering SNVs existed in the reads with alternative alleles (< 25%), and the read depth in founders < 3 within a trio 710 1561 632
Confirmed SNVs by Sanger sequencing (4/13) (1/11) (2/12)
The PL scores for each genotype > 20, 0 and > 0, the PL scores for each genotype in both parents should be 0, > 20 and > 20 130 642 80
Filtering SNVs uncovered by both forward and reverse reads 82 313 52
Manual examination 26 20 16
Confirmed SNVs by Sanger sequencing (20/22) (8/9) (10/11)