Table 2.

Overall summary of alignments.

	CTL	DN	P (DN vs. CTL)*
	Mean (SD), range	Mean (SD), range
Number of input reads	5.71 × 107 (8.50 × 106) 3.91 × 107–7.75 × 107	5.90 × 107 (1.15 × 107) 4.15 × 107–9.10 × 107	0.49
Average input read length	138	138	—
Number of uniquely mapped reads	4.6 × 107 (7.29 × 106) 3.17 × 107–5.88 × 107	4.89 × 107 (8.40 × 106) 3.57 × 107–6.73 × 107	0.17
Uniquely mapped reads (%)	80.47 (3.75) 73.85–85.92	83.29 (3.99) 72.3–88.62	0.009
Average mapped length	137.39 (0.42) 136.10–137.71	137.45 (0.41) 135.93–137.71	0.58
Number of splices: Total	1.62 × 107 (4.93 × 106) 5.67 × 106–2.45 × 107	1.72 × 107 (3.35 × 106) 1.00 × 107–2.38 × 107	0.37
Number of splices: Annotated (sjdb)	1.60 × 107 (4.91 × 106) 5.51 × 106–2.43 × 107	1.70 × 107 (3.33 × 106) 9.86 × 106–2.35 × 107	0.38
Number of splices: GT/AG	1.61 × 107 (4.90 × 106) 5.59 × 106–2.44 × 107	1.71 × 107 (3.33 × 106) 9.92 × 106–2.36 × 107	0.38
Number of splices: GC/AG	9.38 × 104 (2.83 × 104) 3.37 × 104–1.42 × 105	1.09 × 105 (13.37 × 104) 7.05 × 104–1.52 × 105	0.03
Number of splices: AT/AC	7.31 × 103 (2.18 × 103) 2.46 × 103–1.13 × 104	9.38 × 103 (1.95 × 103) 5.41 × 103–1.49 × 104	0.0004
Number of splices: Non-canonical	2.79 × 104 (8.77 × 103) 1.44 × 104–4.91 × 104	2.77 × 104 (8.62 × 103) 1.76 × 104–5.24 × 104	0.92
Mismatch rate per base (%)	0.28 (0.14) 0.15–0.66	0.25 (0.12) 0.15–0.68	0.32
Deletion rate per base (%)	0.002 (0.004) 0–0.01	0.001 (0.004) 0–0.01	0.49
Deletion average length	1.68 (0.32) 1.35–2.66	1.72 (0.29) 1.41–2.78	0.65
Insertion rate per base (%)	0.005 (0.008) 0–0.03	0.003 (0.007) 0–0.03	0.38
Multi-Mapping Reads:
Number of reads mapped to multiple loci	7.09 × 106 (1.34 × 106) 4.89 × 106–1.03 × 107	6.32 × 106 (2.01 × 106) 3.27 × 106–1.29 × 107	0.10
% of reads mapped to multiple loci	12.46 (1.65) 9.61–15.87	10.64 (2.15) 7.26–16.89	0.0008
Number of reads mapped to too many loci	6.16 × 105 (4.96 × 105) 1.31 × 105–1.98 × 106	4.85 × 105 (3.25 × 105) 1.45 × 105–1.66 × 106	0.25
Unmapped Reads:
% of reads unmapped: too many mismatches	0	0	—
% of reads unmapped: too short	5.32 (2.21) 2.99–11.82	4.71 (2.29) 2.63–13.22	0.32

^*Welch’s t-test.