Table 1.

Mapping statistics of sequenced reads from unamplified and amplified libraries

Method	Replicate	Platform	Library type	Total reads	Mapped (%)	Duplicatesa (%)	Properb (%)	Both mapped (%)	Median insert (bp)	Median coverage
Unamplified	1	HiSeq	Short	41 688 676	99.7	0.8	98.1	99.5	285	38
	2	HiSeq	Short	16 333 732	89.4	0.6	88	89.3	357	13
Phi	1	HiSeq	Short	48 501 916	99.4	0.7	98	98.8	224	46
	2	HiSeq	Short	20 656 296	95.2	0.8	88.6	93.7	349	18
Tre	1	HiSeq	Short	44 481 270	99.3	1.1	97.6	98.7	237	40
	2	HiSeq	Short	25 188 788	96.2	0.7	92	95.3	328	22
Rap	1	HiSeq	Short	26 277 398	89.3	2.8	71.6	80.1	248	15
	2	HiSeq	Short	22 278 134	82.5	35.7	60	73.7	308	3
Unamplified	1	HiSeq	Long	60 856 860	99.5	9	97.2	99.1	2631	41
	2	MiSeq	Long	2 551 720	86.4	1	79.1	85.4	2136	2
Phi	1	HiSeq	Long	61 735 210	99.5	3.5	81.5	99.2	2576	39
	2	MiSeq	Long	2 760 576	99.3	1.2	80.2	98.9	2025	2
Tre	1	HiSeq	Long	55 842 586	99.4	3.4	82.6	99	2285	29
	2	MiSeq	Long	2 999 856	99.4	1	73	98.9	2094	2
Rap	1	HiSeq	Long	58 443 656	99.4	7.6	92.1	99	2591	35
	2	MiSeq	Long	3 914 622	99	6.6	91.8	98.7	2121	2

All percentages are relative to total number of reads in each replicate.

^aReads that are identical copies of other reads and have exact mapped coordinates on the genome.

^bReads mapped in the correct orientation and at a distance corresponding to that predicted by the fragment library size.