. Author manuscript; available in PMC: 2016 Aug 1.

Published in final edited form as: Nat Biotechnol. 2016 Feb 1;34(3):303–311. doi: 10.1038/nbt.3432

Table 1.

Summary of phasing results.

Phased whole genome sequencing	NA12878^a	NA12877^a	NA12882^a	NA20847^b	Patient 1532 Normal^c	Patient 1532 Tumor^c
Coverage	37	34	36	32	31	32
% aligned	97	97	96	95	96	96
% duplication	1.38	1.38	1.19	6.45	0.5	0.7
Relative genomic equivalents per partition	0.0015	0.002	0.0019	0.0044	0.0015	0.0011
% barcodes correctly assigned	92	87	85	91	88	86
Effective barcode diversity	111808	151552	126326	144442	136888	125694
Number of molecules (Million)	15.0	34.5	23.4	43.7	30.0	20.6
Length-weighted mean molecules length (kb)	60.53	40.20	47.35	75.69	44.35	38.31
% SNPs phased	99	97	99	98	95	95
% genes phased (<100 kb)	97	92	97	95	93	91
N50 phase block (kb)	2834.44	890.08	1726.40	2577.04	1570.40	962.11
Longest phase block (kb)	14557.82	7016.43	11545.49	12729.94	8729.79	6706.66
SNV short switch error rate (%)	0.01%	0.48%	0.20%	0.93%	N/A	N/A
SNV long switch error rate (%)	0.01%	0.03%	0.02%	0.09%	N/A	N/A

Phased exome sequencing	NA12878^a	NA12877^a	NA12882^a	NA20847^b	NCI-H2228
Coverage	239	497	443	185	244
% bases on target	57	62	59	62	52
% aligned	99	99	99	99	99
% duplication	8.09	18.03	13.79	4.76	8.26
Relative genomic equivalents per partition	0.0007	0.0010	0.0011	0.0008	0.0007
% barcodes correctly assigned	92	92	92	87	87
Effective barcode diversity	149170	138086	150115	154682	121906
% genes phased (<100 kb)	95	95	96	92	N/A
N50 phase block (kb)	136.54	103.42	113.65	83.94	N/A
Longest phase block (kb)	2086.24	1217.01	1199.03	957.57	N/A
SNV short switch error rate (%)	0.47%	1.10%	0.99%	1.36%	N/A
SNV long switch error rate (%)	0.05%	0.11%	0.07%	0.06%	N/A

. Ground-truth is from Cleary et. al., 2014¹⁵.

. Ground-truth is from Kitzman et. al., 2011¹.

. Ground-truth is from GATK call of 50× whole genome sequencing of these samples from our analysis.