Walk finds ptsI-1 with"min_non_zero_depth": 4, and "median_depth": 26,
The reported sequence mapps to ptsI-1 when mapped against the reference panel with bwa mem.
DNA_sequence_identity 92% & Protein_identity 97%
Sample is in /well/iqbal/people/ronaldj/NIS/fastqs/SRR1970018/
Cortex binary in /well/iqbal/people/ronaldj/NIS/cortex/SRR1970018/
Atlas_Output is in /well/iqbal/people/ronaldj/NIS/jsons/SRR1970018/log_atlas.out
Luckily for me, ptsI isn't relevant for me because it has no resistances linked to it. Only R with mutations inactivating gene/downregulating expression. So no hurry. But it's an interesting bug nonetheless.
Walk finds ptsI-1 with
"min_non_zero_depth": 4, and "median_depth": 26,
The reported sequence mapps to ptsI-1 when mapped against the reference panel with bwa mem. DNA_sequence_identity 92% & Protein_identity 97%But Genotype says:
Sample is in /well/iqbal/people/ronaldj/NIS/fastqs/SRR1970018/ Cortex binary in /well/iqbal/people/ronaldj/NIS/cortex/SRR1970018/ Atlas_Output is in /well/iqbal/people/ronaldj/NIS/jsons/SRR1970018/log_atlas.out
This happens in 4717 of 4835 Salmonella samples