Table 1.

Illumina GAII reads and mapping statistics

			Filtered Readsa		Mapped Readsb		Uniquely Mapped Readsc				% Uniquely Mapping to Trimmed Amplicons
Set	Sample	PCR Method	Number	Bases	HG18	Full Ampliconsd	HG18	Full Ampliconsd	Primer Trimmed Amplicons	Exonic Target	Filtered Reads	Mapped Reads	Uniquely Mapped Reads	% of Filtered Reads Mapping on the Exon
457	NA11832	Traditional	1496088	53.86 Mb	50.29 Mb	48.06 Mb	49.24 Mb	47.57 Mb	44.47 Mb	25.35 Mb	83.44%	89.37%	90.31%	47.06%
	NA11832	Microdroplet	1673982	60.26 Mb	56.39 Mb	44.70 Mb	52.99 Mb	44.23 Mb	41.46 Mb	21.47 Mb	69.53%	74.31%	78.24%	35.63%
	NA11992	Traditional	1213396	43.68 Mb	39.33 Mb	37.39 Mb	38.46 Mb	37.01 Mb	35.59 Mb	21.55 Mb	82.31%	91.42%	92.53%	49.34%
	NA11992	Microdroplet	1367394	49.23 Mb	43.83 Mb	30.09 Mb	39.81 Mb	29.71 Mb	28.45 Mb	16.01 Mb	58.55%	65.76%	71.47%	32.53%
	NA12006	Traditional	1256622	45.24 Mb	41.84 Mb	39.64 Mb	40.99 Mb	39.27 Mb	37.49 Mb	21.59 Mb	83.66%	90.45%	91.45%	47.72%
	NA12006	Microdroplet	1148454	41.34 Mb	37.83 Mb	30.00 Mb	35.43 Mb	29.67 Mb	28.15 Mb	15.82 Mb	68.86%	75.26%	79.46%	38.27%
	NA18505	Traditional	1222820	44.02 Mb	40.77 Mb	38.17 Mb	39.83 Mb	37.77 Mb	36.63 Mb	22.00 Mb	84.09%	90.81%	91.95%	49.97%
	NA18505	Microdroplet	1116948	40.21 Mb	36.06 Mb	30.36 Mb	34.36 Mb	30.05 Mb	29.21 Mb	15.87 Mb	73.40%	81.84%	85.01%	39.46%
	NA18517e	Traditional	838226	30.18 Mb	28.12 Mb	26.35 Mb	27.41 Mb	26.04 Mb	24.99 Mb	14.89 Mb	83.81%	89.93%	91.17%	49.33%
	NA18517e	Microdroplet	587958	21.17 Mb	18.12 Mb	13.04 Mb	16.40 Mb	12.87 Mb	12.37 Mb	6.88 Mb	59.16%	69.12%	75.41%	32.49%
	NA18489	Traditional	1429866	51.48 Mb	46.90 Mb	44.44 Mb	45.97 Mb	44.03 Mb	41.08 Mb	23.36 Mb	80.56%	88.42%	89.36%	45.37%
	NA18489	Microdroplet	1885186	67.87 Mb	63.50 Mb	56.18 Mb	60.79 Mb	55.62 Mb	51.75 Mb	27.18 Mb	77.03%	82.32%	85.14%	40.06%
	All Samples	Traditional	7457018	268.45 Mb	247.24 Mb	234.10 Mb	241.91 Mb	231.69 Mb	220.25 Mb	128.72 Mb	82.04%	89.08%	91.04%	47.95%
	All Samples	Microdroplet	7779922	280.08 Mb	255.74 Mb	204.22 Mb	239.77 Mb	202.15 Mb	191.39 Mb	103.23 Mb	68.36%	74.84%	79.82%	36.86%
3976	NA18858	Microdroplet	10603854	381.74 Mb	325.57 Mb	293.89 Mb	309.65 Mb	289.97 Mb	245.20 Mb	122.87 Mb	64.23%	76.30%	79.19%	32.19%

^a- High quality reads from Illumina Pipeline 1.3

^b- Number of bases from filtered reads that were mapped by Maq, non-unique reads are randomly placed at one of the multiple locations

^c- Maq mapping score of 20 or greater, corresponding to a 1% chance of being incorrectly mapped.

^d-Amount of sequence mapping to amplicons including primer sequences

^e- NA18517 had fewer reads than the other 5 samples for both traditional and microdroplet PCR. This was likely a technical issue with both library preparations that is independent of PCR method and DNA quality.