HISAT2 summary stats: Total pairs: 20329409 Aligned concordantly or discordantly 0 time: 2234518 (10.99%) Aligned concordantly 1 time: 16733610 (82.31%) Aligned concordantly >1 times: 1025961 (5.05%) Aligned discordantly 1 time: 335320 (1.65%) Total unpaired reads: 4469036 Aligned 0 time: 3118502 (69.78%) Aligned 1 time: 1208415 (27.04%) Aligned >1 times: 142119 (3.18%) Overall alignment rate: 92.33%