Table 3. Summary of S1 and S2 scores for viral reference sequences.

Aligner	PA (percentage of aligned reads (non-junctions)) (%)	PAj (percentage of aligned reads (junctions)) (%)	non-junctions (%)	(junctions) (%)	S1	S2
Novoalign	99.96±0.04	21.62±0.89	99.92±0.01	92.52±1.18	99.94±0.02	44.73±0.96
BFAST	99.94±0.03	99.97±0.08	98.82±0.95	70.16±7.92	99.38±0.48	83.75±4.73
SHRiMP2	99.61±0.12	75.07±2.00	98.90±0.06	77.48±0.51	99.26±0.07	76.27±1.04
BLAST	98.93±0.09	99.53±0.18	97.41±0.06	70.26±1.26	98.17±0.06	83.63±0.75
BWASW	98.6±0.13	98.45±0.39	95.96±0.04	69.76±1.17	97.27±0.07	82.87±0.71
GSNAP	96.87±0.29	97.17±0.37	97.03±0.10	89.55±2.18	96.95±0.15	93.28±1.15
BWAMEM	96.83±0.20	94.24±1.73	96.7±0.15	69.2±1.00	96.77±0.13	80.76±0.94
Bowtie2	93.21±0.38	90.23±0.96	99.49±0.03	70.07±0.50	96.30±0.20	79.51±0.51
STAR	93.74±0.33	97.63±0.65	98.79±0.04	97.56±0.33	96.23±0.17	97.59±0.36
BLAT	96.22±0.34	96.95±0.18	95.01±0.15	83.09±1.64	95.61±0.19	89.75±0.89
BWA	34.67±1.58	1.82±0.77	99.94±0.06	96.18±1.10	58.86±1.34	13.23±2.80

Shows the summary of alignment results aggregated over four viral genomes for non-mutated viral reference sequences and sorted by S1 score. The average alignment accuracy for reads crossing splice junctions () and those not crossing splice junctions () is defined in the Materials and Methods section.