24hr timepoint of 1L M9/1% dextrose CONTINUOUS FED BATCH fermentation in 2L Sartorius Biostat, feed rate 1g/hr dextrose, set to 30% DO.
Quality Metrics:
| Time0 | 5/20/18 Putida_ML5_set8 | which Time0s the sample was compared to |
| cor12 | 0.19 | rank correlation(fit1, fit2), where fit1 is fitness for the first half (10-50%) and fit2 is fitness for the second half (50-90%) of each gene |
| maxFit | 6.28 | The maximum fitness value |
| opcor | 0.17 | rank correlation(upstream gene, downstream gene) over pairs that are adjacent and likely to be in the same operon |
| adjcor | 0.06 | like opcor but for adjacent genes that are not on the same strand |
| gccor | -0.00 | linear correlation of gene fitness and gene GC content |
| mad12 | 0.30 | median absolute difference of fit1, fit2 |
| mad12c | 1.00 | median absolute difference of log count for 1st and 2nd half of genes in this sample |
| mad12c_t0 | 0.97 | like mad12c but for the Time0s |
| gMed | 61 | median reads per gene in this sample |
| gMedt0 | 554 | median reads per gene in the Time0 sample |
| gMean | 437 | mean reads per gene in this sample |
| nMapped | 3.669 M | #reads for this sample that corresponded to a known strain (in millions) |
| nPastEnd | 0.006 M | #reads that corresponded to a strain that has an insertion within the suicide vector instead of within the genome. |
| nGenic | 2.090 M | #reads that lie within central 10-90% of a gene |
| nUsed | 2.089 M | #reads used to estimate gene fitness (genic and enough coverage for strain and for gene) |
Specific Phenotypes
For 6 genes in this experiment