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 | ||