Summary¶
The Criteria Tables¶
This is what you want. Download the complete quality criteria table:
📋 Download complete filtered metrics
Here are the first few rows of the quality metrics:
| species | metric | lower_bounds | upper_bounds |
|---|---|---|---|
| Xanthomonas_euvesica | N50 | 52000.0 | |
| Xanthomonas_euvesica | no_of_contigs | 270.0 | |
| Xanthomonas_euvesica | GC_Content | 64.0 | 66.0 |
| Xanthomonas_euvesica | Completeness | 96.0 | |
| Xanthomonas_euvesica | Contamination | 3.0 |
Showing 5 of 2128 rows.
Summary Statistics¶
Statistics on distribution for each metric, for each species:
Species Count Summary¶
Breakdown of genomes filtered and retained by using these metrics:
| species | original_count | filtered_out_count | final_count |
|---|---|---|---|
| Salmonella enterica | 644703 | 21033 | 623670 |
| Escherichia coli | 399884 | 11441 | 388443 |
| Mycobacterium tuberculosis | 180095 | 8811 | 171284 |
| Staphylococcus aureus | 121428 | 4269 | 117159 |
| Streptococcus pneumoniae | 121054 | 3349 | 117705 |
| Campylobacter jejuni | 94890 | 3463 | 91427 |
| Klebsiella pneumoniae | 72964 | 2230 | 70734 |
| Listeria monocytogenes | 66720 | 2606 | 64114 |
| Neisseria gonorrhoeae | 57364 | 1905 | 55459 |
| Streptococcus pyogenes | 45861 | 1751 | 44110 |
| Pseudomonas aeruginosa | 43394 | 1459 | 41935 |
| Streptococcus agalactiae | 37375 | 1109 | 36266 |
| Enterococcus faecium | 36574 | 1084 | 35490 |
| Neisseria meningitidis | 35852 | 1499 | 34353 |
| Campylobacter coli | 35173 | 1220 | 33953 |
| Clostridium difficile | 29278 | 1146 | 28132 |
| Acinetobacter baumannii | 28284 | 918 | 27366 |
| Vibrio cholerae | 13069 | 527 | 12542 |
| Haemophilus influenzae | 12553 | 522 | 12031 |
| Enterococcus faecalis | 9673 | 254 | 9419 |
| ... and 284 more rows |
📊 Download complete species counts table
Summary Visualizations¶
Main summary plots and visualizations:
- Metric Range Completeness
- Metric Range Contamination
- Metric Range Gc Content
- Metric Range Genome Size
- Metric Range N50
- Metric Range Total Coding Sequences
- Metric Range No Of Contigs
Additional Summary Plots¶
Detailed analysis plots from the summary analysis:
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