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) |