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Table 8 False negative variants in NA12878 relative to the ASD panel callset

From: Analytical validation of whole exome and whole genome sequencing for clinical applications

Position Variant Truth genotype Called in Would be reviewed Note
Exome
chr10:89720907 T>G T/G 4/7 No Called, but filtered in some replicates for MQ
chr12:2614070 G>T G/T 6/7 Yes (silent) Called, but filtered in one replicate
chrX:15863648 GA>G GA/G 0/7 No Not called in any replicate; 10 bp homopolymer
chrX:135115669 GA>G GA/G 0/7 No Called, but filtered in two replicates; 11 bp homopolymer
chrX:152954025 A>G G/G 6/7 Yes (UTR) Low depth region
chrX:153287314 TG>T TG/T 0/7 Yes (UTR) Called, but filtered in all replicates for QD; 10 bp homopolymer
Genome
chr5:176639217 TA>T TA/T 0/6 No Not called in any replicate; 13 bp homopolymer
chr7:146805220 AT>A AT/A 0/6 No Not called in any replicate; 11 bp homopolymer
chr10:89720633 CT>C CT/C 0/6 No Not called in any replicate; 15 bp homopolymer
chr10:89720907 T>G T/G 0/6 No Called, but filtered in all replicates
chr11:70348852 G>CG CG/CG 0/6 No Called, but as heterozygous in all replicates; inside 12 bp homopolymer
chrX:15863648 GA>G GA/G 0/6 No Not called in any replicate; 10 bp homopolymer
chrX:132888207 TA>T TA/T 3/6 No Not called in three replicates; 16 bp homopolymer
chrX:135067675 G>C G/C 5/6 Yes (missense) Not called in one replicate
chrX:135115669 GA>G GA/G 1/6 No Called in one replicate; 11 bp homopolymer
chrX:153287314 TG>T TG/T 1/6 Yes (UTR) Called in one replicate; 10 bp homopolymer
chrX:153357614 TA>T TA/T 1/6 No Called in one replicate; 13 bp homopolymer
  1. Most common error mode is single base deletions in homopolymer regions. Each variant is annotated as to whether it would be further reviewed in interpretations workflow (Yes) or automatically filtered out from further consideration (No).