Table S2. False positive SNV calls from sequencing the genome-in-a-bottle sample NA12878 Gene gDNA (GRCh37) cDNA Coding effect Frequency Read quality* chr3:g.53752770 NM_000720.3:c.1538+2T>G p.? 6/8 Low QD value (0.47-4.94) CACNA1D chr1:g.103468336 NM_080629.2:c.2046T>G p.= 6/8 Low QD value (0.66-2.31) COL11A1 chr1:g.215960153 NM_206933.2:c.10246T>G p.Cys3416Gly 2/8 Low QD value (0.47-0.52) USH2A chr19:g.45206971 NM_001039213.3:c.382+8A>C p.? 1/8 Low QD value (2.06) CEACAM16 chr22:g.38155502 NM_138632.2: c.1264A>C p.? 1/8 Low QD value (0.28) TRIOBP chr5:g.90459600 NM_032119.3:c.18804T>G p.= 1/8 Low QD value (0.61) ADGRV1 * Low read quality with QD value<13.3) and extreme strand bias in BAM files (97-100% reads from one strand)
Table S2. False positive SNV calls from sequencing the genome-in-a-bottle sample NA12878 Gene gDNA (GRCh37) cDNA Coding effect Frequency Read quality* CACNA1D chr3:g.53752770 NM_000720.3:c.1538+2T>G p.? 6/8 Low QD value (0.47-4.94) COL11A1 chr1:g.103468336 NM_080629.2:c.2046T>G p.= 6/8 Low QD value (0.66-2.31) USH2A chr1:g.215960153 NM_206933.2:c.10246T>G p.Cys3416Gly 2/8 Low QD value (0.47-0.52) CEACAM16 chr19:g.45206971 NM_001039213.3:c.382+8A>C p.? 1/8 Low QD value (2.06) TRIOBP chr22:g.38155502 NM_138632.2: c.1264A>C p.? 1/8 Low QD value (0.28) ADGRV1 chr5:g.90459600 NM_032119.3:c.18804T>G p.= 1/8 Low QD value (0.61) * Low read quality with QD value<13.3) and extreme strand bias in BAM files (97-100% reads from one strand)
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