Table 1.

DeLoxer output quality statistics

	Number of reads	Percentage of reads (%)	Fragment size (mean ± SD)	Size after trimming (mean ± SD)
Total 2 × 100 reads	78 607 373	100.00
Mate-paired reads (LoxP positive)	22 494 162	28.62		79 ± 22
Uniquely aligned pairs	18 970 394	100.00
True mate-paired reads	18 951 404	99.90	2313 ± 812
Paired-end reads	7216	0.04	400 ± 78
Short fragments	1359	0.01	95 ± 66
Non-unique alignment	2 488 148
Unaligned	1 035 620
Duplicate reads	5 518 899	29.09
Paired-end reads (LoxP positive)	22 424 011	28.53		78 ± 22
Uniquely aligned pairs	17 963 827	100.00
True paired-end reads	12 677 878	70.57	256 ± 40
Mate-paired reads	2663	0.01	3299 ± 2261
Short fragments	5 283 278	29.41	168 ± 32
Non-unique alignment	3 478 415
Unaligned	981 769
Duplicate reads	5 008 216	27.88
LoxP negative, low quality	5 517 705	7.02
LoxP negative, quality filtered	22 288 114	28.35		83 ± 18
Uniquely aligned pairs	12 409 334	100.00
Mate-paired reads	11 567 200	93.21	2279 ± 813
Paired-end reads	46 637	0.38	290 ± 64
Short fragments	777 291	6.26	61 ± 17
Non-unique alignment	1 613 963
Unaligned	8 264 817
Duplicate reads	3 243 252	26.14
Single reads (LoxP positive)	5 820 905	7.41
Both reads too short (LoxP positive)	62 476	0.08

Data generated by sequencing a 3-kb mate-paired S. cerevisiae DNA library (prepared using 14 cycles of PCR), sequenced in one Illumina HiSeq flowcell lane.