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 |