Table 2 (abstract P41).

Example of summary statistics comparing Atlas genotype calls with differing allele fraction thresholds with GATK calls.

Genotype	GATK	ATLAS (ORIGINALS)	ATLAS DP>=10 0.25<0/1>0.75	ATLAS DP>=10 0.1<0/1>0.9	ATLAS DP>=10 0.1<0/1>0.75
0/0	1,793,394,356	1,788,668,240	1,778,668,240	1,778,668,240	1,778,668,240
0/1	138,744,203	69,153,666	112,165,710	147,763,797	124,056,267
1/1	79,407,733	60,398,312	73,417,546	49,710,016	73,423,295
Het / hom	1.75	1.14	1.53	2.97	1.69
Total	2,011,546,292	1,908,220,218	1,964,251,496	1,976,142,053	1,976,147,802
Concordant Genotypes	GATK + ATLAS (ORIGINALS)	GATK + ATLAS (0.25<0/1>0.75)	GATK + ATLAS (0.1<0/1>0.9)	GATK + ATLAS (0.1<0/1>0.75)
0/0	914,737,638	1,021,734,445	1,050,682,661	1,049,337,470
0/1	39,133,931	72,422,398	74,278,418	75,570,661
1/1	17,017,045	45,077,505	33,993,884	45,368,697
Het/hom	2.30	1.61	2.19	1.67
Total	970,888,614	1,139,234,348	1,158,954,963	1,170,276,828