Table 1.
Summary Illumina sequencing statistics
| Strain | Growth environment | Replicate | Total number of reads | Number of aligned reads |
|---|---|---|---|---|
| NEM316 |
Milk |
1 |
29,089,124 |
27,350,545 |
| NEM316 |
Milk |
2 |
40,554,665 |
38,161,713 |
| NEM316 |
Milk |
3 |
35,497,113 |
33,357,550 |
| NEM316 |
Broth |
1 |
23,013,312 |
21,250,407 |
| NEM316 |
Broth |
2 |
23,145,072 |
21,484,496 |
| CCUG 37738 |
Milk |
1 |
20,106,316 |
7,516,242 |
| CCUG 37738 |
Milk |
2 |
16,800,749 |
6,494,892 |
| CCUG 37738 |
Milk |
3 |
28,308,724 |
11,028,696 |
| CCUG 37738 |
Broth |
1 |
44,274,054 |
19,357,826 |
| CCUG 37738 |
Broth |
2 |
27,893,761 |
11,196,100 |
| CCUG 37738 |
Broth |
3 |
17,763,818 |
7,925,653 |
| FSL S3-586 |
Milk |
1 |
29,138,705 |
8,033,022 |
| FSL S3-586 |
Milk |
2 |
27,373,266 |
4,909,064 |
| FSL S3-586 |
Milk |
3 |
16,688,288 |
6,786,044 |
| FSL S3-586 |
Broth |
1 |
15,172,203 |
4,505,824 |
| FSL S3-586 | Broth | 2 | 21,093,103 | 6,750,884 |
The average proportion of reads passing the Illumina quality filter for each replicate was 94.6% (range = 93-97%). The number of aligned reads excludes reads ambiguously aligned to multiple locations within the respective genome sequence.