Benchmarking SNPs Whole Exome
Case	Number of bases	Truth total	TP	FP	FN	TN = TotalBases - (TP + FN + FP)	TotalNegative  = TN + FP	NPA = TN/(Total Negative)	Precision	Recall
NA12878	71152019	57822	57128	417	671	71093803	71094220	100.00	99.28	98.84
NA24143	65657646	55975	55378	341	574	65601353	65601694	100.00	99.39	98.97
NA24149	65597266	55518	54861	453	635	65541317	65541770	100.00	99.18	98.86
NA24385	65948744	56068	55190	437	844	65892273	65892710	100.00	99.21	98.49
NA24631	66988987	56948	56395	334	551	66931707	66932041	100.00	99.41	99.03
	Benchmarking INDELs Whole Exome
Case	Number of bases	Truth total	TP	FP	FN	TN = TotalBases - (TP + FN + FP)	TotalNegative  = TN + FP	NPA = TN/(Total Negative)	Precision	Recall
NA12878	71152019	5318	4927	1138	407	71145547	71146685	100.00	81.24	92.35
NA12878 - Indels 1 - 10	71152019	5114	4722	1123	392	71145782	71146905	100.00	80.79	92.33
NA12878 - Indels 11 - 20	71152019	207	194	10	13	71151802	71151812	100.00	95.10	93.72
NA12878 - Indels 21 - 50	71152019	52	50	4	2	71151963	71151967	100.00	92.59	96.15
NA24143	65657646	5388	4942	1254	460	65650990	65652244	100.00	79.76	91.46
NA24143 - Indels 1 - 10	65657646	5171	4735	1239	436	65651236	65652475	100.00	79.26	91.57
NA24143 - Indels 11 - 20	65657646	206	189	9	17	65657431	65657440	100.00	95.45	91.75
NA24143 - Indels 21 - 50	65657646	84	77	6	7	65657556	65657562	100.00	92.77	91.67
NA24149	65597266	5290	4869	1191	441	65590765	65591956	100.00	80.35	91.66
NA24149 - Indels 1 - 10	65597266	5116	4694	1175	422	65590975	65592150	100.00	79.98	91.75
NA24149 - Indels 11 - 20	65597266	185	172	12	13	65597069	65597081	100.00	93.48	92.97
NA24149 - Indels 21 - 50	65597266	68	62	4	6	65597194	65597198	100.00	93.94	91.18
NA24385	65948744	5362	4793	1346	594	65942011	65943357	100.00	78.07	88.92
NA24385 - Indels 1 - 10	65948744	5167	4602	1333	565	65942244	65943577	100.00	77.54	89.07
NA24385 - Indels 11 - 20	65948744	204	181	8	23	65948532	65948540	100.00	95.77	88.73
NA24385 - Indels 21 - 50	65948744	67	61	5	6	65948672	65948677	100.00	92.42	91.04
NA24631	66988987	5805	5281	848	524	66982334	66983182	100.00	86.16	90.97
NA24631 - Indels 1 - 10	66988987	5563	5057	837	506	66982587	66983424	100.00	85.80	90.90
NA24631 - Indels 11 - 20	66988987	186	178	4	8	66988797	66988801	100.00	97.80	95.70
NA24631 - Indels 21 - 50	66988987	82	72	7	10	66988898	66988905	100.00	91.14	87.80
	Benchmarking SNPs Coding Exons
Case	Number of bases	Truth total	TP	FP	FN	TN = TotalBases - (TP + FN + FP)	TotalNegative  = TN + FP	NPA = TN/(Total Negative)	Precision	Recall
NA12878	13728555	7803	7783	4	20	13720748	13720752	100.00	99.95	99.74
NA24143	12549224	7470	7465	3	5	12541751	12541754	100.00	99.96	99.93
NA24149	12538042	7495	7485	15	9	12530533	12530548	100.00	99.8	99.88
NA24385	12626866	7452	7447	7	5	12619407	12619414	100.00	99.91	99.93
NA24631	12808688	7591	7583	22	8	12801075	12801097	100.00	99.71	99.89
	Benchmarking INDELs Coding Exons
Case	Number of bases	Truth total	TP	FP	FN	TN = TotalBases - (TP + FN + FP)	TotalNegative  = TN + FP	NPA = TN/(Total Negative)	Precision	Recall
NA12878	13728555	156	152	14	4	13728385	13728399	100.00	91.57	97.44
NA12878 - Indels 1 - 10	13728555	145	141	13	4	13728397	13728410	100.00	91.56	97.24
NA12878 - Indels 11 - 20	13728555	7	7	0	0	13728548	13728548	100.00	100.00	100.00
NA12878 - Indels 21 - 50	13728555	5	5	1	0	13728549	13728550	100.00	83.33	100.00
NA24143	12549224	163	154	17	9	12549044	12549061	100.00	90.06	94.48
NA24143 - Indels 1 - 10	12549224	154	145	17	9	12549053	12549070	100.00	89.51	94.16
NA24143 - Indels 11 - 20	12549224	8	8	0	0	12549216	12549216	100.00	100.00	100.00
NA24143 - Indels 21 - 50	12549224	3	3	0	0	12549221	12549221	100.00	100.00	100.00
NA24149	12538042	163	160	13	4	12537865	12537878	100.00	92.49	97.55
NA24149 - Indels 1 - 10	12538042	157	153	13	4	12537872	12537885	100.00	92.17	97.45
NA24149 - Indels 11 - 20	12538042	8	8	0	0	12538034	12538034	100.00	100.00	100.00
NA24149 - Indels 21 - 50	12538042	1	1	0	0	12538041	12538041	100.00	100.00	100.00
NA24385	12626866	157	150	14	7	12626695	12626709	100.00	91.46	95.54
NA24385 - Indels 1 - 10	12626866	145	138	12	7	12626709	12626721	100.00	92.00	95.17
NA24385 - Indels 11 - 20	12626866	9	9	0	0	12626857	12626857	100.00	100.00	100.00
NA24385 - Indels 21 - 50	12626866	3	3	2	0	12626861	12626863	100.00	60.00	100.00
NA24631	12808688	162	151	18	11	12808508	12808526	100.00	89.35	93.21
NA24631 - Indels 1 - 10	12808688	154	144	18	10	12808516	12808534	100.00	88.89	93.51
NA24631 - Indels 11 - 20	12808688	5	5	0	0	12808683	12808683	100.00	100.00	100.00
NA24631 - Indels 21 - 50	12808688	5	4	0	1	12808683	12808683	100.00	100.00	80.00