| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T396 |
0-113 |
Sentence |
denotes |
For trimming of the reads (i.e., removal of P7 Illumina adapter sequences), cutadapt (version 2.8) (42) was used. |
| T397 |
114-250 |
Sentence |
denotes |
For validation of the origin of the sequence of the LAMP product (fig. S4A), 107 reads were randomly selected and used for the analysis. |
| T398 |
251-388 |
Sentence |
denotes |
Reads were mapped to the SARS-CoV-2 reference genome (NC_045512.2) (43), using bwa-mem with default settings (version 0.7.17-r1188) (44). |
| T399 |
389-478 |
Sentence |
denotes |
Virus genome coverage was determined with the samtools depth command (version 1.10) (45). |
| T400 |
479-564 |
Sentence |
denotes |
Using bwa-mem, 80.6% of reads could be mapped to the virus genome (fig. S4, B and C). |
| T401 |
565-654 |
Sentence |
denotes |
To analyze the remaining sequences, a k-mer analysis using a custom script was performed. |
| T402 |
655-830 |
Sentence |
denotes |
Using 9-mers, this matched 93.5% of the nonmapped reads with a maximal Levenshtein distance of two to one of the LAMP primers or their reverse complement sequences (fig. S4D). |
| T403 |
831-927 |
Sentence |
denotes |
This is explained by the fact that LAMP products can consist of complex sequence rearrangements. |
