Table 1 Quality control and assignment rates from Trimmomatic and BBSplit.
Treatment | Replicate | Raw input read pairs | Reads retained by Trimmomatic (%) | In planta reads assigned to S. scler. by BBSplit (%) | Final read pairs |
|---|---|---|---|---|---|
In vitro | 1 | 51,429,980 | 94.9 | NA | 47,609,295 |
In vitro | 2 | 43,993,597 | 94.9 | NA | 40,898,891 |
In vitro | 3 | 42,595,015 | 95.2 | NA | 39,702,901 |
B. napus | 1 | 42,067,707 | 91 | 25.7 | 9,595,914 |
B. napus | 2 | 39,650,442 | 90.7 | 7.5 | 2,630,108 |
B. napus | 3 | 45,312,584 | 92.9 | 44 | 18,079,428 |
L. angustifolius | 1 | 39,982,586 | 92.7 | 26.4 | 9,487,026 |
L. angustifolius | 2 | 40,510,004 | 92.4 | 83.9 | 30,699,672 |
L. angustifolius | 3 | 47,604,827 | 93.9 | 48 | 20,783,466 |
