TABLE 3.
Microbial read size distribution. All percentages are relative to the total reads (or sequencing yield) of the quality filtered reads, prior to removal of human reads
| Qiagen Genomic Tip (GT) | Phenol–chloroform (PC) | Agarose encasement (AE) | ||||
|---|---|---|---|---|---|---|
| GT_1 | GT_2 | PC_1 | PC_2 | AE_1 | AE_2 | |
| All reads | ||||||
| Number of reads | 2,052,300 | 3,681,083 | 2,008,795 | 4,338,575 | 739,186 | 962,065 |
| Sequencing yield (Gbp) | 1.440 | 1.959 | 1.311 | 1.972 | 0.767 | 1.133 |
| All microbial reads | ||||||
| Number of reads | 468,071 | 1,007,070 | 344,348 | 905,391 | 248,809 | 376,332 |
| % | 22.81 | 27.36 | 17.14 | 20.87 | 33.66 | 39.12 |
| Sequencing yield (Gbp) | 0.532 | 0.759 | 0.285 | 0.436 | 0.362 | 0.669 |
| % | 36.93 | 38.77 | 21.74 | 22.12 | 47.21 | 59.09 |
| N50 | 2810 | 1929 | 1116 | 449 | 2524 | 3649 |
| L50 | 38,513 | 62,126 | 34,874 | 155,142 | 38,768 | 52,182 |
| Median length (bp) | 468 | 326 | 427 | 307 | 782 | 837 |
| Longest microbial reads (bp) | 73,029 | 90,424 a | 163,320 | 180,460 | 68,189 | 116,730 |
| The top hit for the longest microbial read on NCBI’s nr database (identity/alignment) | Streptococcus salivarius (93.6%/99%) | Streptococcus salivarius (92%/98%) a | Streptococcus sp. (89.9%/81%) | Veillonella dispar (88.7%/69%) | Veillonella nakazawae (90.2%/89%) | Prevotella histicola (92.5%/96%) |
| Microbial reads >2.5 kb | ||||||
| Number of reads | 43,173 | 49,572 | 13,752 | 10,182 | 39,270 | 82,221 |
| % | 2.10 | 1.35 | 0.68 | 0.23 | 5.31 | 8.55 |
| Sequencing yield (Gbp) | 0.278 | 0.352 | 0.109 | 0.117 | 0.182 | 0.426 |
| % | 19.32 | 17.98 | 8.29 | 5.92 | 23.77 | 37.58 |
a
Showing the second longest read as the first longest read (92,515 bp) had no hits on NCBI.