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 |