Table 3 Reasons for low confident bases in ACMG genes

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