Table 2.
RNAseq overview and mapping
| Characteristics* |
STM 2683 |
STM 4661 |
||||
|---|---|---|---|---|---|---|
| Control (TY) | Zinc (0.5 mM) | Cadmium (0.025 mM) | Control (TY) | Zinc (0.5 mM) | Cadmium (0.025 mM) | |
|
Total read number |
81,308,886 (100%) |
73,773,403 (100%) |
68,813,483 (100%) |
72,111,015 (100%) |
74,765,870 (100%) |
81,587,705 (100%) |
|
Nb of unmapped reads |
1,949,038 (2.40%) |
2,031,313 (2.75%) |
1,892,551 (2.75%) |
1,623,268 (2.25%) |
1,718,059 (2.30%) |
1,776,552 (2.18%) |
|
Nb of reads mapped at least once |
79,359,848 (97.60%) |
71,742,090 97.25%) |
66,920,932 (97.25%) |
70,487,747 (97.75%) |
73,047,811 (97.70%) |
79,811,153 (97.82%) |
|
Nb of reads mapped on rRNA |
41,428,635 (50.95%) |
30,531,652 (41.39%) |
32,224,949 (46.83%) |
39,466,389 (54.73%) |
37,982,860 (50.80%) |
47,500,946 (58.22%) |
|
rRNA depletion rate ** |
94.3 |
96.1 |
95.1 |
93.3 |
94.3 |
92.3 |
|
Nb of reads kept (only reads uniquely mapped) |
78,729,668 (96.83%) |
71,178,074 (96.48%) |
66,380,750 (96.46%) |
70,090,461 (97.20%) |
72,683,423 (97.21%) |
79,431,748 (97.36%) |
|
Nb of reads kept against chromosome |
78,147,818 (96.11%) |
70,490,263 (95.55%) |
65,861,607 (95.71%) |
69,802,581 (96.80%) |
72,348,246 (96.77%) |
79,118,286 (96.97%) |
|
Nb of reads kept against plasmid |
581,850 (0.72%) |
687,811 (0.93%) |
519,143 (0.75%) |
287,880 (0.40%) |
335,177 (0.45%) |
313,462 (0.38%) |
| Nb of reads kept for downstream analyses*** | 37,301,033 (45.86%) | 40,646,422 (55.10%) | 34,155,801 (49.64%) | 30,624,072 (42.47%) | 34,700,563 (46.41%) | 31,930,802 (39.14%) |
* Numbers of reads per sample obtained after mapping analyses are indicated together with their proportions relative to the total read numbers in parentheses.
** Estimated rRNA substitution rate, considering that 95% of the RNA was initially composed of rRNA.
***Only reads that uniquely mapped, and did not map rRNAs.