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Table 3 Reasons for low confident bases in ACMG genes

From: Medical implications of technical accuracy in genome sequencing

Reason for low confidence Percentage of bases
CNVs or other SVs that have been reported in dbVar for NA12878 47
STRs in RepSeqSTRdb 34
Regions with known segmental duplications 15
Simple Repeats from repeat masker 1.7
<3 datasets have at least 5 reads with mapping quality >10 1.3
Abnormal allele balance 0.17
Unresolved conflicting genotypes after arbitration 0.03
Calls with support from <3 datasets after arbitration 0.0082
Local alignment problems 0.0041