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Updated Practical 6 MAG analyses (markdown) authored by Luis H Orellana (Coto)'s avatar Luis H Orellana (Coto)
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Practical-6-MAG-analyses.md
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...@@ -33,10 +33,13 @@ See the output file generated by checkM (e.g., checkm_MaxBin-selected-20.txt). I ...@@ -33,10 +33,13 @@ See the output file generated by checkM (e.g., checkm_MaxBin-selected-20.txt). I
``` ```
Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity Bin Id Marker lineage # genomes # markers # marker sets 0 1 2 3 4 5+ Completeness Contamination Strain heterogeneity
ACF_bins.001 o__Rickettsiales (UID3809) 83 324 211 145 175 4 0 0 0 50.38 1.03 75.00 U.maxbin.012 f__Rhodobacteraceae (UID3360) 56 582 313 44 496 40 2 0 0 92.73 9.08 17.39
ACF_bins.002 k__Bacteria (UID203) 5449 99 53 80 19 0 0 0 0 27.67 0.00 0.00 U.maxbin.007 f__Flavobacteriaceae (UID2845) 53 548 298 33 468 43 4 0 0 94.32 8.36 14.55
ACF_bins.003 k__Bacteria (UID203) 5449 99 53 89 6 4 0 0 0 10.12 0.69 75.00 U.maxbin.006 f__Flavobacteriaceae (UID2845) 53 548 298 15 255 235 35 8 0 96.50 61.93 87.11
ACF_bins.004 o__Rickettsiales (UID3809) 83 324 211 130 130 58 6 0 0 56.95 22.74 36.84 U.maxbin.002 f__Flavobacteriaceae (UID2845) 53 548 298 11 484 52 0 1 0 96.70 10.81 18.97
U.maxbin.001 s__algicola (UID2847) 33 496 263 26 461 9 0 0 0 94.53 2.66 88.89
Q.maxbin.008 k__Bacteria (UID203) 5449 104 58 36 32 31 4 1 0 68.12 39.26 4.08
Q.maxbin.006 k__Bacteria (UID203) 5449 104 58 22 27 55 0 0 0 65.52 27.43 0.00
``` ```
What do you think about the quality of these bins? In the following activities we will be analyzing some of them using anvi'o. For now, let's analyze them a little further. We can ask checkM to give us a bit more taxonomical information using the `checkm tree` function incorporated in checkM. What do you think about the quality of these bins? In the following activities we will be analyzing some of them using anvi'o. For now, let's analyze them a little further. We can ask checkM to give us a bit more taxonomical information using the `checkm tree` function incorporated in checkM.
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