Table 3.
Results of the control and the common process of the main study. Filters, assembly and taxonomic assignment of five patient tumor samples with former BAC histology (AT1–5)
| Quality and hg19 filters | Main study | |||||||
|---|---|---|---|---|---|---|---|---|
| Samples | AT1 | AT2 | AT3 | AT4 | AT5 | 5 samples AT1-5 | ||
| Remaining reads | 579,994 | 618,449 | 619,414 | 613,570 | 433,398 | 2,864,825 | ||
| Control process | ||||||||
| Mapping (bowtie2) | Nber of reads vs control samples | 357,616 (62 %) | 407,370 (66 %) | 555,964 (89 %) | 476,430 (78 %) | 396 ,251 (91 %) | 2,193,631 (76 %) | |
| Remaining reads | 222,378 | 211,079 | 63,450 | 137,140 | 37,147 | 671,194 | ||
| Common process | ||||||||
| Global assembly (SPAdes) | Contigs with reads from this sample | 269 (45 %) | 307 (51 %) | 278 (46 %) | 324 (54 %) | 285 (48 %) | 596 (100 %) | |
| Contigs only with reads from this sample | 23 (3.8 %) | 41 (6.8 %) | 31 (5.2 %) | 32 (5.3 %) | 57 (9.5 %) | 45 (7.5 %) | ||
| Taxonomic assignation (blastn) | Contigs without taxonomy. Total length | 54 contigs 4599 bases | 66 contigs 13,688 bases | 56 contigs 10,662 bases | 70 contigs 15,426 bases | 74 contigs 16,785 bases | 162 contigs 36,852 bases (20 %) | |
| Taxonomy count | NA | NA | NA | NA | NA | 96 % Eukaryota including 76 % Hominidae. 4 % vectors | ||