Table 1.

Results of alignment of raw data and data trimmed by Trimmomatic from both datasets

Dataset/aligner	Reads	Toleranta	Strictb
Dataset 1 with Bowtie2 aligner
Unfiltered	11 008 190	9 018 810	6 401 927
Trimmomatic—adapters only	11 008 150	9 117 952	6 510 253
Trimmomatic—SW	9 456 826	9 079 434	8 086 905
Trimmomatic—MI	9 456 826	9 116 627	8 748 376
Trimmomatic—adapters and SW	9 456 819	9 150 361	8 111 470
Trimmomatic—adapters and MI	9 456 126	9 153 375	8 748 401
Dataset 1 with BWA aligner
Unfiltered	11 008 190	8 750 851	7 834 544
Trimmomatic—adapters only	11 008 150	8 864 884	7 942 198
Trimmomatic—adapters and SW	9 456 819	9 110 831	8 810 063
Trimmomatic—adapters and MI	9 456 126	9 145 423	9 056 403
Dataset 2 with BWA aligner
Unfiltered	801 192	60 010	11 592
Trimmomatic—adapters only	801 164	121 926	68 177
Trimmomatic—adapters and SW	655 075	628 867	590 729
Trimmomatic—adapters and MI	658 796	639 740	634 779

Note: Adapter trimming, where done, used palindrome mode. Best values per dataset and aligner are indicated in bold. MI indicates Maximum Information mode, and SW indicates Sliding Window mode.

^aAlignment allowing some mismatches and/or INDELs. See Supplementary Methods for more details.

^bAligned when no mismatches or INDELs were allowed.